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<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>
<DIV style="font-family: 'Times New Roman',Times,serif">


<DIV style="width: 100%; border-bottom: 2pt solid black; font-size: 1pt">&nbsp;</DIV>
<DIV style="width: 100%; border-bottom: 1pt solid black; font-size: 1pt">&nbsp;</DIV>




<DIV align="center" style="font-size: 14pt; margin-top: 12pt"><B>UNITED STATES SECURITIES AND EXCHANGE COMMISSION</B>
</DIV>

<DIV align="center" style="font-size: 12pt"><B>Washington, D.C. 20549</B>
</DIV>

<DIV align="center" style="font-size: 18pt; margin-top: 12pt"><B>FORM S-8</B>
</DIV>


<DIV align="center" style="font-size: 12pt; margin-top: 12pt"><B>REGISTRATION STATEMENT UNDER THE<BR>
SECURITIES ACT OF 1933</B>
</DIV>

<DIV align="center" style="font-size: 24pt; margin-top: 12pt"><B>SGX Pharmaceuticals, Inc.</B>
</DIV>

<DIV align="center" style="font-size: 10pt"><I>(Exact name of registrant as specified in its charter)</I></DIV>


<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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<TR valign="bottom">
    <TD width="47%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="47%">&nbsp;</TD>
</TR>
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<TR valign="bottom">
    <TD align="center" valign="top"><B>Delaware</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>06-1523147</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><I>(State or other jurisdiction of incorporation or</I>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><I>(I.R.S. Employer Identification No.)</I></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><I>organization)</I></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>10505 Roselle Street</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>92121</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>San Diego, California</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><I>(Zip Code)</I></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><I>(Address of Principal Executive Offices)</I></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 12pt"><B>2005 Equity Incentive Plan<BR>
2005 Employee Stock Purchase Plan<BR>
2005 Non-Employee Directors&#146; Stock Option Plan</B><BR>
<I>(Full title of the plans)</I></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 12pt"><B>Michael Grey<BR>
President and CEO<BR>
SGX Pharmaceuticals, Inc.<BR>
10505 Roselle Street<BR>
San Diego, CA 92121</B><BR>
<I>(Name and address of agent for services)</I></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 12pt"><B>(858)&nbsp;558-4850</B><BR>
<I>(Telephone number, including area code, of agent for service)</I></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 12pt"><B><I>Copies to:</I></B></DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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<TR valign="bottom">
    <TD width="47%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="47%">&nbsp;</TD>
</TR>
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<TR valign="bottom">
    <TD align="center" valign="top"><B>Annette North, Esq.</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>Frederick T. Muto, Esq.</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>General Counsel and</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>J. Patrick Loofbourrow, Esq.</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>Corporate Secretary</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>Cooley Godward Kronish LLP</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>SGX Pharmaceuticals, Inc.</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>4401 Eastgate Mall</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>10505 Roselle Street</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>San Diego, CA 92121</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>San Diego, CA 92121</B>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top"><B>(858)&nbsp;550-6000</B></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top"><B>(858)&nbsp;558-4850</B></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
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</TABLE>
</DIV>
<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Indicate by check mark whether the registrant is a large accelerated filer, an accelerated
filer, a non-accelerated filer, or a smaller reporting company. See the definitions of &#147;large
accelerated filer,&#148; &#147;accelerated filer&#148; and &#147;smaller reporting company&#148; in Rule&nbsp;12b-2 of the
Exchange Act. (Check one):
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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<TR valign="bottom" style="font-size: 0pt">
    <TD width="22%">&nbsp;</TD>
    <TD width="3%">&nbsp;</TD>
    <TD width="22%">&nbsp;</TD>
    <TD width="3%">&nbsp;</TD>
    <TD width="22%">&nbsp;</TD>
    <TD width="3%">&nbsp;</TD>
    <TD width="22%">&nbsp;</TD>
</TR>
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<TR valign="bottom">
    <TD align="left" valign="top" nowrap>Large accelerated filer
<FONT face="Wingdings">&#111;</FONT></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top" nowrap>Accelerated filer
<FONT face="Wingdings">&#111;</FONT></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top" nowrap>Non-accelerated filer <FONT face="Wingdings">&#111;</FONT></TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top" nowrap>Smaller reporting company <FONT face="Wingdings">&#254;</FONT></TD>
</TR>
<TR valign="bottom">
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top" nowrap>(Do not check if a smaller reporting company)</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>CALCULATION OF REGISTRATION FEE</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
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<TR valign="bottom">
    <TD width="1%">&nbsp;</TD>
    <TD width="47%">&nbsp;</TD>
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    <TD width="1%">&nbsp;</TD>
    <TD width="21%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD><!-- VRule -->
    <TD width="1%">&nbsp;</TD>
    <TD width="4%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD><!-- VRule -->
    <TD width="1%">&nbsp;</TD>
    <TD width="12%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD><!-- VRule -->
    <TD width="1%">&nbsp;</TD>
    <TD width="6%">&nbsp;</TD>

    <TD width="1%">&nbsp;</TD>
</TR><TR style="font-size: 1px" valign="bottom">
    <TD nowrap align="left" colspan="15" style="border-bottom: 3px double #000000">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Proposed</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Maximum</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Proposed Maximum</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD nowrap align="center">Title of Each Class of Securities to</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Amount to be</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Offering</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Aggregate</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Amount of</TD>
    <TD width="1%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">    <TD width="1%">&nbsp;</TD>

    <TD nowrap align="center">be Registered</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Registered (1)</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Price per Share (2)</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Offering Price (2)</TD>
    <TD style="border-right: 2px solid #000000">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">Registration Fee</TD>
    <TD width="1%">&nbsp;</TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom">
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
                    <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock issuable under the
2005 Equity Incentive Plan (par
value $0.001 per share)</DIV></TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">500,000 shares(3)</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$1.355</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$677,500</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$26.63</TD>
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock issuable under the
2005 Employee Stock Purchase Plan
(par value $0.001 per share)</DIV></TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">150,000 shares(4)</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$1.355</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$203,250</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$&nbsp;7.98</TD>
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px">Common Stock issuable under the
2005 Non-Employee Directors&#146; Stock Option Plan
(par value $0.001) per share</DIV></TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">62,500 (5)</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">$1.355</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">$&nbsp;84,688</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">$&nbsp;3.33</TD>
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000"><DIV style="margin-left:15px; text-indent:-15px"><B>Total</B></DIV></TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">712,500 shares</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>
    <TD align="center" valign="top" style="border-top: 2px solid #000000">N/A</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">$965,438</TD>
    <TD style="border-right: 2px solid #000000; border-top: 2px solid #000000">&nbsp;</TD>
    <TD style="border-top: 2px solid #000000">&nbsp;</TD>

<TD align="center" valign="top" style="border-top: 2px solid #000000">$37.94</TD>
    <TD width="1%" style="border-top: 2px solid #000000">&nbsp;</TD>
</TR>
<TR style="font-size: 1px" valign="bottom">
    <TD nowrap align="left" colspan="15" style="border-top: 3px double #000000">&nbsp;</TD>
</TR>

<!-- End Table Body -->
</TABLE>
</DIV>



<TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
<TR style="font-size: 3pt">
    <TD width="3%">&nbsp;</TD>
    <TD width="1%"></TD>
    <TD width="96"></TD>
</TR>

<TR valign="top">
    <TD nowrap align="left">(1)</TD>
    <TD>&nbsp;</TD>
    <TD>Pursuant to Rule 416(a) under the Securities Act of 1933, as amended
(the &#147;<B><I>Securities Act</I></B>&#148;), this Registration Statement on Form S-8 <BR>
(&#147; <B><I>Registration Statement </I></B>&#148;) also registers any additional shares of the
Registrant&#146;s common stock, par value $0.001 per share (the &#147; <B><I>Common
Stock </I></B>&#148;), as may become issuable under the plans as a result of any
stock split, stock dividend, recapitalization or other similar
transaction.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(2)</TD>
    <TD>&nbsp;</TD>
    <TD>Estimated solely for the purpose of calculating the amount of the
registration fee pursuant to Rule 457(c) and Rule&nbsp;457(h)(1) under the
Securities Act. The price per share and aggregate offering price are
based upon the average of the high and low prices of the Registrant&#146;s
Common Stock on May&nbsp;21, 2008, as reported on the Nasdaq Global Market.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(3)</TD>
    <TD>&nbsp;</TD>
    <TD>Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant&#146;s 2005 Equity
Incentive Plan (the &#147; <B><I>2005 EIP </I></B>&#148;) on January&nbsp;1, 2008 pursuant to an
&#147;evergreen&#148; provision contained in the 2005 EIP. Pursuant to such
provision, on January 1<SUP style="font-size: 85%; vertical-align: text-top">st</SUP> of each year commencing in 2007
and ending on (and including) January&nbsp;1, 2015, the number of shares
authorized for issuance under the 2005 EIP is automatically increased
by a number equal to the lesser of (i)&nbsp;three and one half percent
(3<SUP style="font-size: 85%; vertical-align: text-top">1/2</SUP>%) of the total number of shares of Common Stock
outstanding on December&nbsp;31<SUP style="font-size: 85%; vertical-align: text-top">st</SUP> of the preceding calendar year (rounded
up to the nearest whole share), (ii)&nbsp;500,000
shares of Common Stock or (iii)&nbsp;an amount determined by the Registrant&#146;s Board of Directors or
a duly authorized committee of the Board of Directors.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(4)</TD>
    <TD>&nbsp;</TD>
    <TD>Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant&#146;s 2005 Employee
Stock Purchase Plan (the &#147; <B><I>2005 ESPP </I></B>&#148;) on January&nbsp;1, 2008 pursuant to
an &#147;evergreen&#148; provision contained in the 2005 ESPP. Pursuant to such
provision, on the first day of the Registrant&#146;s fiscal year beginning
in 2007 and ending in (and including) 2015, the number of shares
authorized for issuance under the 2005 ESPP is automatically increased
by a number equal to the lesser of (i)&nbsp;one percent (1%) of the total number
of shares of Common Stock outstanding on December&nbsp;31<SUP style="font-size: 85%; vertical-align: text-top">st</SUP> of
the preceding year (rounded to the nearest whole share), (ii)&nbsp;150,000
shares of Common Stock, or (iii)&nbsp;an amount determined by the
Registrant&#146;s Board of Directors or a duly authorized committee of the
Board of Directors.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(5)</TD>
    <TD>&nbsp;</TD>
    <TD>Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant&#146;s 2005
Non-Employee Directors&#146; Stock Option Plan (the &#147;<B><I>Directors&#146; Plan</I></B>&#148;) on
January&nbsp;1, 2008 pursuant to an &#147;evergreen&#148; provision contained in the
Directors&#146; Plan. Pursuant to such provision, on the first day of the
Registrant&#146;s fiscal year beginning in 2007 and ending in (and
including) 2015, the number of shares authorized for issuance under
the Directors&#146; Plan is automatically increased by a number equal to
the lesser of (i)&nbsp;the aggregate number of shares of Common Stock
subject to options granted under the Directors&#146; Plan as initial grants
and annual grants during the immediately preceding fiscal year, or
(ii)&nbsp;an amount determined by the Registrant&#146;s Board of Directors or a
duly authorized committee of the Board of Directors.</TD>
</TR>

</TABLE>



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<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>INCORPORATION BY REFERENCE OF CONTENTS OF<BR>
REGISTRATION STATEMENTS ON FORM S-8 NO. 333-131428</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This Registration Statement is being filed for the purpose of increasing the number of
securities of the same class as other securities for which a Registration Statement on Form S-8 of
the Registrant relating to the same benefit plans is effective. The Registrant previously
registered shares of its Common Stock for issuance under the 2005 EIP, the 2005 ESPP and the
Directors&#146; Plan under a Registration Statement on Form S-8 filed with the Securities and Exchange
Commission on February&nbsp;1, 2006 (File No.&nbsp;333-131428). Pursuant to General Instruction E to Form
S-8, this Registration Statement hereby incorporates by reference the contents of the Registration
Statement referenced above (File No.&nbsp;333-131428).
</DIV>

<!-- TOC -->
<A name="toc"><DIV align="CENTER" style="page-break-before:always"><U><B>TABLE OF CONTENTS</B></U></DIV></A>

<P><CENTER>
<TABLE border="0" width="90%" cellpadding="0" cellspacing="0">
<TR>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="3%"></TD>
	<TD width="76%"></TD>
</TR>
<TR><TD colspan="9"><A HREF="#000">INCORPORATION BY REFERENCE OF CONTENTS OF REGISTRATION STATEMENTS ON FORM S-8 NO. 333-131428</A></TD></TR>
<TR><TD colspan="9"><A HREF="#001">EXHIBITS</A></TD></TR>
<TR><TD colspan="9"><A HREF="#002">SIGNATURES</A></TD></TR>
<TR><TD colspan="9"><A HREF="#003">POWER OF ATTORNEY</A></TD></TR>
<TR><TD colspan="9"><A HREF="#004">EXHIBIT INDEX</A></TD></TR>
<TR><TD colspan="9"><A HREF="a41079exv5w1.htm">EXHIBIT 5.1</A></TD></TR>
<TR><TD colspan="9"><A HREF="a41079exv23w1.htm">EXHIBIT 23.1</A></TD></TR>
</TABLE>
</CENTER>
<!-- /TOC -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>




<!-- link1 "EXHIBITS" -->
<DIV align="left"><A NAME="001"></A></DIV>
<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>EXHIBITS</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="3%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="92%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Exhibit</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Number</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Description</B></TD>
</TR>
<TR valign="bottom">
    <TD>&nbsp;</TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1<SUP style="font-size: 85%; vertical-align: text-top">(1)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Registrant&#146;s Amended and Restated Certificate of Incorporation.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.2<SUP style="font-size: 85%; vertical-align: text-top">(2)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Registrant&#146;s Amended and Restated Bylaws.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.3<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Common Stock Certificate of the Registrant.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Opinion of Cooley Godward Kronish LLP.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Cooley Godward Kronish LLP. Reference is made to Exhibit
5.1.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Power of Attorney. Reference is made to the signature page of this
Form&nbsp;S-8.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.1<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Equity Incentive Plan and Form of Stock Option Agreement and Form
of Stock Option Grant Notice thereunder.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.2<SUP style="font-size: 85%; vertical-align: text-top">(4)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit
Agreement for Executive Officers under the Registrant&#146;s 2005 Equity
Incentive Plan.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.3<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Employee Stock Purchase Plan and Form of Offering Document
thereunder.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.4<SUP style="font-size: 85%; vertical-align: text-top">(5)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Non-Employee Directors&#146;
Stock Option Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>



<DIV align="left">
<DIV style="font-size: 3pt; margin-top: 16pt; width: 18%; border-top: 1px solid #000000">&nbsp;</DIV>
</DIV>

<TABLE width="100%" border="0" cellpadding="0" cellspacing="0" style="font-size: 10pt">
<TR>
    <TD width="3%"></TD>
    <TD width="1%"></TD>
    <TD width="96"></TD>
</TR>

<TR valign="top">
    <TD nowrap align="left">(1)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Registration Statement on Form
S-1 (File No.&nbsp;33-128059) filed with the Commission on September&nbsp;2,
2005, and incorporated herein by reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(2)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Annual Report on Form 10-K
(File No.<u>000-51745</u>) for the year ended December&nbsp;31, 2006 filed with
the Commission on March&nbsp;30, 2007, and incorporated herein by
reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(3)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to Amendment No.&nbsp;4 to the Registrant&#146;s
Registration Statement on Form S-1 (File No.&nbsp;33-128059) filed with the
Commission on January&nbsp;4, 2006, and incorporated herein by reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(4)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Annual Report on Form 10-K
(File No.&nbsp;000-51745) for the year ended December&nbsp;31, 2005 filed with
the Commission on March&nbsp;31, 2006, and incorporated herein by
reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(5)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Quarterly Report on Form 10-Q
(File No.&nbsp;000-51745) filed with the Commission on August&nbsp;14, 2007, and incorporated herein by
reference.</TD>
</TR>

</TABLE>


<P align="center" style="font-size: 10pt"><!-- Folio -->&nbsp;<!-- /Folio -->
</DIV>

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<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>


<DIV style="font-family: 'Times New Roman',Times,serif">





<!-- link1 "SIGNATURES" -->
<DIV align="left"><A NAME="002"></A></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>SIGNATURES</B>
</DIV>


<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the requirements for
filing on Form S-8 and has duly caused this Registration Statement to be signed on its behalf by
the undersigned, thereunto duly authorized, in the City of San Diego, State of California, on May
27, 2008.
</DIV>

<TABLE width="100%" border="0" cellspacing="0" cellpadding="0" style="font-size: 10pt">
<TR>
    <TD width="48%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="1%">&nbsp;</TD>
    <TD width="35%">&nbsp;</TD>
    <TD width="15%">&nbsp;</TD>
</TR>
<TR>
    <TD valign="top" align="left">&nbsp;</TD>
    <TD colspan="3" align="left"><B>SGX PHARMACEUTICALS, INC.</B><BR>
&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD valign="top">By:&nbsp;&nbsp;</TD>
    <TD colspan="2" style="border-bottom: 1px solid #000000" align="left">/s/ Michael Grey
&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left">Michael Grey&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR><TR>
    <TD align="left">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD colspan="2" align="left">Chief Executive Officer&nbsp;</TD>
    <TD>&nbsp;</TD>
</TR>
<TR>
    <TD colspan="5">&nbsp;</TD>
</TR>
</TABLE>
<!-- link1 "POWER OF ATTORNEY" -->
<DIV align="left"><A NAME="003"></A></DIV>
<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>POWER OF ATTORNEY</B>
</DIV>



<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>KNOW ALL PERSONS BY THESE PRESENTS</B>, that each person whose signature appears below constitutes
and appoints TODD MYERS and MICHAEL GREY, and each of them, his or her true and lawful
attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and
in his or her name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to file the same, with
all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange
Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he or she might or could do in
person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or either of
them, or their or his substitutes or substitute, may lawfully do or cause to be done by virtue
hereof.
</DIV>

<DIV align="left" style="font-size: 10pt; margin-top: 6pt">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration
Statement has been signed by the following persons in the capacities and on the date indicated.</DIV>


<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="35%">&nbsp;</TD>
    <TD width="2%">&nbsp;</TD>
    <TD width="35%">&nbsp;</TD>
    <TD width="2%">&nbsp;</TD>
    <TD width="26%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="center"><B>Signature</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Title</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Date</B></TD>
</TR>
<TR valign="bottom">
    <TD>&nbsp;</TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Michael Grey
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Michael Grey
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">President, Chief Executive Officer and<BR>
Member of the Board of Directors<BR>
<I>(Principal Executive Officer)</I>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Todd Myers
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Todd Myers, C.P.A.
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Chief Financial Officer<BR>
<I>(Principal Financial and Accounting<BR>
Officer)</I>
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008&nbsp;</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Christopher S. Henney
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Christopher S. Henney, Ph.D., D.Sc.
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Chairman of the Board of Directors
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Louis C. Bock
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Louis C. Bock
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Member of the Board of Directors
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Karin Eastham
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Karin Eastham, C.P.A.
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Member of the Board of Directors
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Jean-Francois Formela, M.D.
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Member of the Board of Directors
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">/s/ Joseph Turner
<DIV style="font-size: 1pt; border-top: 1px solid #000000">&nbsp;</DIV>
Joseph Turner
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Member of the Board of Directors
</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">May&nbsp;27, 2008</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD align="center" valign="bottom"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
    <TD>&nbsp;</TD>
    <TD align="center" valign="top">&nbsp;</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>


<P align="center" style="font-size: 10pt"><!-- Folio -->&nbsp;<!-- /Folio -->
</DIV>

<!-- PAGEBREAK -->
<P><HR noshade><P>
<H5 align="left" style="page-break-before:always"><A HREF="#toc">Table of Contents</A></H5><P>

<DIV style="font-family: 'Times New Roman',Times,serif">

<!-- link1 "EXHIBIT INDEX" -->
<DIV align="left"><A NAME="004"></A></DIV>

<DIV align="center" style="font-size: 10pt; margin-top: 18pt"><B>EXHIBIT INDEX</B>
</DIV>

<DIV align="center">
<TABLE style="font-size: 10pt" cellspacing="0" border="0" cellpadding="0" width="100%">
<!-- Begin Table Head -->
<TR valign="bottom">
    <TD width="3%">&nbsp;</TD>
    <TD width="5%">&nbsp;</TD>
    <TD width="92%">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Exhibit</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center">&nbsp;</TD>
</TR>
<TR style="font-size: 8pt" valign="bottom">
    <TD nowrap align="left"><B>Number</B></TD>
    <TD>&nbsp;</TD>
    <TD nowrap align="center"><B>Description</B></TD>
</TR>
<TR valign="bottom">
    <TD>&nbsp;</TD>
</TR>

<!-- End Table Head -->
<!-- Begin Table Body -->
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.1<SUP style="font-size: 85%; vertical-align: text-top">(1)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Registrant&#146;s Amended and Restated Certificate of Incorporation.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.2<SUP style="font-size: 85%; vertical-align: text-top">(2)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Registrant&#146;s Amended and Restated Bylaws.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">4.3<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Common Stock Certificate of the Registrant.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">5.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Opinion of Cooley Godward Kronish LLP.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Independent Registered Public Accounting Firm.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">23.2
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Consent of Cooley Godward Kronish LLP. Reference is made to Exhibit&nbsp;5.1.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">24.1
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Power of Attorney. Reference is made to the signature page of this Form&nbsp;S-8.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.1<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Equity Incentive Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.2<SUP style="font-size: 85%; vertical-align: text-top">(4)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit
Agreement for Executive Officers under the Registrant&#146;s 2005 Equity
Incentive Plan.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.3<SUP style="font-size: 85%; vertical-align: text-top">(3)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Employee Stock Purchase Plan and Form of Offering Document thereunder.</TD>
</TR>
<TR valign="bottom"><!-- Blank Space -->
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">&nbsp;</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">&nbsp;</TD>
</TR>
<TR valign="bottom">
    <TD valign="top"><DIV style="margin-left:0px; text-indent:-0px">99.4<SUP style="font-size: 85%; vertical-align: text-top">(5)</SUP>
</DIV></TD>
    <TD>&nbsp;</TD>
    <TD align="left" valign="top">2005 Non-Employee Directors&#146;
Stock Option Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.</TD>
</TR>
<!-- End Table Body -->
</TABLE>
</DIV>



<DIV align="left">
<DIV style="font-size: 3pt; margin-top: 16pt; width: 18%; border-top: 1px solid #000000">&nbsp;</DIV>
</DIV>

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<TR>
    <TD width="3%"></TD>
    <TD width="1%"></TD>
    <TD width="96"></TD>
</TR>

<TR valign="top">
    <TD nowrap align="left">(1)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Registration Statement on Form
S-1 (File No.&nbsp;33-128059) filed with the Commission on September&nbsp;2,
2005, and incorporated herein by reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(2)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Annual Report on Form 10-K
(File No. <u>000-51745</u>) for the year ended December&nbsp;31, 2006 filed with
the Commission on March&nbsp;30, 2007, and incorporated herein by
reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(3)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to Amendment No.&nbsp;4 to the Registrant&#146;s
Registration Statement on Form S-1 (File No.&nbsp;33-128059) filed with the
Commission on January&nbsp;4, 2006, and incorporated herein by reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(4)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Annual Report on Form 10-K
(File No.&nbsp;000-51745) for the year ended December&nbsp;31, 2005 filed with
the Commission on March&nbsp;31, 2006, and incorporated herein by
reference.</TD>
</TR>

<TR style="font-size: 3pt"><TD>&nbsp;</TD></TR>

<TR valign="top">
    <TD nowrap align="left">(5)</TD>
    <TD>&nbsp;</TD>
    <TD>Filed as an exhibit to the Registrant&#146;s Quarterly Report on Form 10-Q
(File No.&nbsp;000-51745) filed with the Commission on August&nbsp;14, 2007, and incorporated herein by
reference.</TD>
</TR>
</TABLE>


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sv8
Table of Contents
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549
FORM S-8
REGISTRATION STATEMENT UNDER THE
SECURITIES ACT OF 1933
SGX Pharmaceuticals, Inc.
(Exact name of registrant as specified in its charter)
Delaware
06-1523147
(State or other jurisdiction of incorporation or
(I.R.S. Employer Identification No.)
organization)
10505 Roselle Street
92121
San Diego, California
(Zip Code)
(Address of Principal Executive Offices)
2005 Equity Incentive Plan
2005 Employee Stock Purchase Plan
2005 Non-Employee Directors' Stock Option Plan
(Full title of the plans)
Michael Grey
President and CEO
SGX Pharmaceuticals, Inc.
10505 Roselle Street
San Diego, CA 92121
(Name and address of agent for services)
(858) 558-4850
(Telephone number, including area code, of agent for service)
Copies to:
Annette North, Esq.
Frederick T. Muto, Esq.
General Counsel and
J. Patrick Loofbourrow, Esq.
Corporate Secretary
Cooley Godward Kronish LLP
SGX Pharmaceuticals, Inc.
4401 Eastgate Mall
10505 Roselle Street
San Diego, CA 92121
San Diego, CA 92121
(858) 550-6000
(858) 558-4850
Indicate by check mark whether the registrant is a large accelerated filer, an accelerated
filer, a non-accelerated filer, or a smaller reporting company. See the definitions of "large
accelerated filer," "accelerated filer" and "smaller reporting company" in Rule 12b-2 of the
Exchange Act. (Check one):
Large accelerated filer
o
Accelerated filer
o
Non-accelerated filer
o
Smaller reporting company
þ
(Do not check if a smaller reporting company)
CALCULATION OF REGISTRATION FEE
Proposed
Maximum
Proposed Maximum
Title of Each Class of Securities to
Amount to be
Offering
Aggregate
Amount of
be Registered
Registered (1)
Price per Share (2)
Offering Price (2)
Registration Fee
Common Stock issuable under the
2005 Equity Incentive Plan (par
value $0.001 per share)
500,000 shares(3)
$1.355
$677,500
$26.63
Common Stock issuable under the
2005 Employee Stock Purchase Plan
(par value $0.001 per share)
150,000 shares(4)
$1.355
$203,250
$ 7.98
Common Stock issuable under the
2005 Non-Employee Directors' Stock Option Plan
(par value $0.001) per share
62,500 (5)
$1.355
$ 84,688
$ 3.33
Total
712,500 shares
N/A
$965,438
$37.94
(1)
Pursuant to Rule 416(a) under the Securities Act of 1933, as amended
(the "
Securities Act
"), this Registration Statement on Form S-8
("
Registration Statement
") also registers any additional shares of the
Registrant's common stock, par value $0.001 per share (the "
Common
Stock
"), as may become issuable under the plans as a result of any
stock split, stock dividend, recapitalization or other similar
transaction.
(2)
Estimated solely for the purpose of calculating the amount of the
registration fee pursuant to Rule 457(c) and Rule 457(h)(1) under the
Securities Act. The price per share and aggregate offering price are
based upon the average of the high and low prices of the Registrant's
Common Stock on May 21, 2008, as reported on the Nasdaq Global Market.
(3)
Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant's 2005 Equity
Incentive Plan (the "
2005 EIP
") on January 1, 2008 pursuant to an
"evergreen" provision contained in the 2005 EIP. Pursuant to such
provision, on January 1
st
of each year commencing in 2007
and ending on (and including) January 1, 2015, the number of shares
authorized for issuance under the 2005 EIP is automatically increased
by a number equal to the lesser of (i) three and one half percent
(3
1/2
%) of the total number of shares of Common Stock
outstanding on December 31
st
of the preceding calendar year (rounded
up to the nearest whole share), (ii) 500,000
shares of Common Stock or (iii) an amount determined by the Registrant's Board of Directors or
a duly authorized committee of the Board of Directors.
(4)
Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant's 2005 Employee
Stock Purchase Plan (the "
2005 ESPP
") on January 1, 2008 pursuant to
an "evergreen" provision contained in the 2005 ESPP. Pursuant to such
provision, on the first day of the Registrant's fiscal year beginning
in 2007 and ending in (and including) 2015, the number of shares
authorized for issuance under the 2005 ESPP is automatically increased
by a number equal to the lesser of (i) one percent (1%) of the total number
of shares of Common Stock outstanding on December 31
st
of
the preceding year (rounded to the nearest whole share), (ii) 150,000
shares of Common Stock, or (iii) an amount determined by the
Registrant's Board of Directors or a duly authorized committee of the
Board of Directors.
(5)
Represents shares of Common Stock that were automatically added to the
shares authorized for issuance under the Registrant's 2005
Non-Employee Directors' Stock Option Plan (the "
Directors' Plan
") on
January 1, 2008 pursuant to an "evergreen" provision contained in the
Directors' Plan. Pursuant to such provision, on the first day of the
Registrant's fiscal year beginning in 2007 and ending in (and
including) 2015, the number of shares authorized for issuance under
the Directors' Plan is automatically increased by a number equal to
the lesser of (i) the aggregate number of shares of Common Stock
subject to options granted under the Directors' Plan as initial grants
and annual grants during the immediately preceding fiscal year, or
(ii) an amount determined by the Registrant's Board of Directors or a
duly authorized committee of the Board of Directors.
INCORPORATION BY REFERENCE OF CONTENTS OF
REGISTRATION STATEMENTS ON FORM S-8 NO. 333-131428
This Registration Statement is being filed for the purpose of increasing the number of
securities of the same class as other securities for which a Registration Statement on Form S-8 of
the Registrant relating to the same benefit plans is effective. The Registrant previously
registered shares of its Common Stock for issuance under the 2005 EIP, the 2005 ESPP and the
Directors' Plan under a Registration Statement on Form S-8 filed with the Securities and Exchange
Commission on February 1, 2006 (File No. 333-131428). Pursuant to General Instruction E to Form
S-8, this Registration Statement hereby incorporates by reference the contents of the Registration
Statement referenced above (File No. 333-131428).
TABLE OF CONTENTS
INCORPORATION BY REFERENCE OF CONTENTS OF REGISTRATION STATEMENTS ON FORM S-8 NO. 333-131428
EXHIBITS
SIGNATURES
POWER OF ATTORNEY
EXHIBIT INDEX
EXHIBIT 5.1
EXHIBIT 23.1
Table of Contents
EXHIBITS
Exhibit
Number
Description
4.1
(1)
Form of Registrant's Amended and Restated Certificate of Incorporation.
4.2
(2)
Form of Registrant's Amended and Restated Bylaws.
4.3
(3)
Form of Common Stock Certificate of the Registrant.
5.1
Opinion of Cooley Godward Kronish LLP.
23.1
Consent of Independent Registered Public Accounting Firm.
23.2
Consent of Cooley Godward Kronish LLP. Reference is made to Exhibit
5.1.
24.1
Power of Attorney. Reference is made to the signature page of this
Form S-8.
99.1
(3)
2005 Equity Incentive Plan and Form of Stock Option Agreement and Form
of Stock Option Grant Notice thereunder.
99.2
(4)
Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit
Agreement for Executive Officers under the Registrant's 2005 Equity
Incentive Plan.
99.3
(3)
2005 Employee Stock Purchase Plan and Form of Offering Document
thereunder.
99.4
(5)
2005 Non-Employee Directors'
Stock Option Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.
(1)
Filed as an exhibit to the Registrant's Registration Statement on Form
S-1 (File No. 33-128059) filed with the Commission on September 2,
2005, and incorporated herein by reference.
(2)
Filed as an exhibit to the Registrant's Annual Report on Form 10-K
(File No.
000-51745
) for the year ended December 31, 2006 filed with
the Commission on March 30, 2007, and incorporated herein by
reference.
(3)
Filed as an exhibit to Amendment No. 4 to the Registrant's
Registration Statement on Form S-1 (File No. 33-128059) filed with the
Commission on January 4, 2006, and incorporated herein by reference.
(4)
Filed as an exhibit to the Registrant's Annual Report on Form 10-K
(File No. 000-51745) for the year ended December 31, 2005 filed with
the Commission on March 31, 2006, and incorporated herein by
reference.
(5)
Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q
(File No. 000-51745) filed with the Commission on August 14, 2007, and incorporated herein by
reference.
Table of Contents
SIGNATURES
Pursuant to the requirements of the Securities Act of 1933, as amended, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the requirements for
filing on Form S-8 and has duly caused this Registration Statement to be signed on its behalf by
the undersigned, thereunto duly authorized, in the City of San Diego, State of California, on May
27, 2008.
SGX PHARMACEUTICALS, INC.
By:
/s/ Michael Grey
Michael Grey
Chief Executive Officer
POWER OF ATTORNEY
KNOW ALL PERSONS BY THESE PRESENTS
, that each person whose signature appears below constitutes
and appoints TODD MYERS and MICHAEL GREY, and each of them, his or her true and lawful
attorney-in-fact and agent, with full power of substitution and resubstitution, for him or her and
in his or her name, place and stead, in any and all capacities, to sign any and all amendments
(including post-effective amendments) to this Registration Statement, and to file the same, with
all exhibits thereto, and other documents in connection therewith, with the Securities and Exchange
Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and
authority to do and perform each and every act and thing requisite and necessary to be done in
connection therewith, as fully to all intents and purposes as he or she might or could do in
person, hereby ratifying and confirming all that said attorneys-in-fact and agents, or either of
them, or their or his substitutes or substitute, may lawfully do or cause to be done by virtue
hereof.
Pursuant to the requirements of the Securities Act of 1933, as amended, this Registration
Statement has been signed by the following persons in the capacities and on the date indicated.
Signature
Title
Date
/s/ Michael Grey
Michael Grey
President, Chief Executive Officer and
Member of the Board of Directors
(Principal Executive Officer)
May 27, 2008
/s/ Todd Myers
Todd Myers, C.P.A.
Chief Financial Officer
(Principal Financial and Accounting
Officer)
May 27, 2008
/s/ Christopher S. Henney
Christopher S. Henney, Ph.D., D.Sc.
Chairman of the Board of Directors
May 27, 2008
/s/ Louis C. Bock
Louis C. Bock
Member of the Board of Directors
May 27, 2008
/s/ Karin Eastham
Karin Eastham, C.P.A.
Member of the Board of Directors
May 27, 2008
Jean-Francois Formela, M.D.
Member of the Board of Directors
May 27, 2008
/s/ Joseph Turner
Joseph Turner
Member of the Board of Directors
May 27, 2008
Table of Contents
EXHIBIT INDEX
Exhibit
Number
Description
4.1
(1)
Form of Registrant's Amended and Restated Certificate of Incorporation.
4.2
(2)
Form of Registrant's Amended and Restated Bylaws.
4.3
(3)
Form of Common Stock Certificate of the Registrant.
5.1
Opinion of Cooley Godward Kronish LLP.
23.1
Consent of Independent Registered Public Accounting Firm.
23.2
Consent of Cooley Godward Kronish LLP. Reference is made to Exhibit 5.1.
24.1
Power of Attorney. Reference is made to the signature page of this Form S-8.
99.1
(3)
2005 Equity Incentive Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.
99.2
(4)
Form of Restricted Stock Unit Grant Notice and Restricted Stock Unit
Agreement for Executive Officers under the Registrant's 2005 Equity
Incentive Plan.
99.3
(3)
2005 Employee Stock Purchase Plan and Form of Offering Document thereunder.
99.4
(5)
2005 Non-Employee Directors'
Stock Option Plan and Form of Stock Option Agreement and Form of
Stock Option Grant Notice thereunder.
(1)
Filed as an exhibit to the Registrant's Registration Statement on Form
S-1 (File No. 33-128059) filed with the Commission on September 2,
2005, and incorporated herein by reference.
(2)
Filed as an exhibit to the Registrant's Annual Report on Form 10-K
(File No.
000-51745
) for the year ended December 31, 2006 filed with
the Commission on March 30, 2007, and incorporated herein by
reference.
(3)
Filed as an exhibit to Amendment No. 4 to the Registrant's
Registration Statement on Form S-1 (File No. 33-128059) filed with the
Commission on January 4, 2006, and incorporated herein by reference.
(4)
Filed as an exhibit to the Registrant's Annual Report on Form 10-K
(File No. 000-51745) for the year ended December 31, 2005 filed with
the Commission on March 31, 2006, and incorporated herein by
reference.
(5)
Filed as an exhibit to the Registrant's Quarterly Report on Form 10-Q
(File No. 000-51745) filed with the Commission on August 14, 2007, and incorporated herein by
reference.