PHARMACOPEIA INC
EX-10.31
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<TYPE>EX-10.31
<SEQUENCE>4
<FILENAME>a03-2221_1ex1031.htm
<DESCRIPTION>EX-10.31
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<p align="right" style="margin:0in 0in .0001pt;text-align:right;"><b><font size="2" face="Times New Roman" style="font-size:10.0pt;font-weight:bold;">Exhibit 10.31</font></b></p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="line-height:12.0pt;margin:0in 0in .0001pt;text-autospace:none;"><font size="2" color="black" face="Tms Rmn" style="color:black;font-size:10.0pt;">* CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILED
SEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITH
RESPECT TO THE OMITTED PORTIONS. </font></p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p align="center" style="margin:0in 0in .0001pt;text-align:center;"><b><font size="2" face="Times New Roman" style="font-size:10.0pt;font-weight:bold;">AMENDMENT NO. 5</font></b></p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">This Amendment
No. 5 (this &#147;Amendment No. 5&#148;) to the Collaboration and License Agreements
effective October 29, 1998 between the parties hereto, as amended previously
(the &#147;1998 Agreements&#148;), is effective as of July 9, 2003 (the &#147;Amendment No. 5
Effective Date&#148;) and by agreement of the parties as of the Amendment No. 5
Effective Date amends the 1998 Agreements as follows:</font></p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">1.</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>All capitalized terms
herein shall have the same meaning as in the 1998 Agreements.</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">2.</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>The parties agree
that as of the Amendment No. 5 Effective Date:</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(i)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>Schering&#146;s and SPL&#146;s
exclusivity with respect to *;</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(ii)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>The Exclusivity Periods
with respect to *;</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(iii)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>*</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(iv)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>Subject to the
provisions of Section 4.5 of the 1998 Agreements, *</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">3.</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>Section 5.2.4 of each
1998 Agreement is hereby amended by adding to the end of such Section of that
1998 Agreement the following:</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(a)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>*</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(b)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>* <u>Interim Period</u>.
Pharmacopeia agrees that, notwithstanding its right under the first sentence of
Section 5.2.4 (as previously amended) to remove FTEs from the Collaboration
beginning * it shall not exercise such right during the Interim Period. The
&#147;Interim Period,&#148; as used herein, shall mean the period beginning *</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(c)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font><u>Staffing and Payment
During Interim Period</u>. During the Interim Period, (i) the parties agree
that Pharmacopeia shall provide, and each of Schering and SPL shall fund, *
FTEs *, (ii) each of Schering and SPL shall pay Pharmacopeia for these * FTEs
at the rate of * and (iii) all other provisions of the 1998 Agreements * shall
remain in full force and effect in accordance with their respective terms. For
the avoidance of doubt, it is understood and agreed by the parties that (A) for
each of the *FTEs assigned to the Collaboration during the Interim Period,
Pharmacopeia shall be entitled to receive the funding set forth in clause (ii)
of the preceding sentence *.</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(d)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>*</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(B)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font><u>Extension
of Collaboration Term</u>. Notwithstanding Section 2.2.1 of the 1998
Agreements, the term of the Collaboration shall be extended until *.</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(C)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>*
<u>Collaboration</u>. In lieu of its rights and the other terms provided under
Section 5.2.4 of the 1998 Agreements (as in effect prior to the Amendment No. 5
Effective Date), Pharmacopeia shall have the right, starting *, to remove FTEs
from the Collaboration * such that the minimum number of Pharmacopeia FTEs
assigned to the Collaboration during the period from *shall be *respectively.
It is understood and agreed that Schering and SPL each shall pay Pharmacopeia
(at the FTE rate in effect under the 1998 Agreements immediately prior to the
Amendment No. 5 Effective Date) for *. In the event that Schering or SPL
requests</p>

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<p align="center" style="font-size:10.0pt;margin:0in 0in .0001pt;text-align:center;">&nbsp;</p>

<p style="margin:0in 0in .0001pt 1.0in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">additional
Pharmacopeia manpower be available to the Collaboration * (i.e., in addition to
the minimum numbers of FTEs set forth in this Section 5.2.4. 1(d)(ii)(C)),
Schering and SPL shall, *which shall be payable in full *.&#148;</font></p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt 1.0in;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">(D)</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font><u>Revocation
of Section 2 of Amendment No. 5</u>. All of the provisions set forth in Section
2 of this Amendment No. 5 shall be revoked and of no force and effect as of the
earlier of *</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="font-size:10.0pt;margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">4.</font><font size="1" style="font-size:8.0pt;">&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160;&#160; </font>The remaining terms
of the 1998 Agreements, except to the extent modified by the terms of this
Amendment, the agreement letter dated March 29, 1999, Amendment No. 1 effective
April 15, 1999, Amendment No. 2 effective October 1, 1999, Amendment No. 3
effective April 17, 2003 and Amendment No. 4 effective May 29, 2003, shall
remain in full force and effect.</p>

<p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<p style="margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">IN WITNESS
WHEREOF, the parties hereto have caused this Amendment No. 5 to be duly
executed by their authorized representatives and delivered in triplicate
originals on the Amendment No. 5 Effective Date.</font></p>

<p style="margin:0in 0in .0001pt;text-indent:.5in;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">&nbsp;</font></p>

<table border="0" cellspacing="0" cellpadding="0" width="100%" style="border-collapse:collapse;width:100.0%;">
 <tr>
  <td width="51%" colspan="4" valign="top" style="padding:0in .7pt 0in .7pt;width:51.92%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">SCHERING
  CORPORATION</font></p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">PHARMACOPEIA,
  INC.</font></p>
  </td>
 </tr>
 <tr>
  <td width="4%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:4.32%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">By:</font></p>
  </td>
  <td width="37%" valign="top" style="border:none;border-bottom:solid windowtext .5pt;padding:0in .7pt 0in .7pt;width:37.4%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">/s/ David
  Poorvin</font></p>
  </td>
  <td width="10%" valign="top" style="padding:0in .7pt 0in .7pt;width:10.2%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="4%" valign="top" style="padding:0in .7pt 0in .7pt;width:4.04%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">By:</font></p>
  </td>
  <td width="32%" valign="top" style="border:none;border-bottom:solid windowtext .5pt;padding:0in .7pt 0in .7pt;width:32.84%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">/s/ Stephen
  A. Spearman</font></p>
  </td>
  <td width="11%" valign="top" style="padding:0in .7pt 0in .7pt;width:11.22%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
 <tr>
  <td width="4%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:4.32%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="47%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:47.6%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">DAVID
  POORVIN, PH.D.</font></p>
  </td>
  <td width="4%" valign="top" style="padding:0in .7pt 0in .7pt;width:4.04%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="44%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:44.06%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">STEPHEN A.
  SPEARMAN, PH.D.</font></p>
  </td>
 </tr>
 <tr>
  <td width="4%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:4.32%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="47%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:47.6%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">Vice
  President</font></p>
  </td>
  <td width="4%" valign="top" style="padding:0in .7pt 0in .7pt;width:4.04%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="44%" colspan="2" valign="top" style="padding:0in .7pt 0in .7pt;width:44.06%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">Executive
  Vice President and<br>
  Chief Operating Officer</font></p>
  </td>
 </tr>
 <tr>
  <td width="51%" colspan="4" valign="top" style="padding:0in .7pt 0in .7pt;width:51.92%;">
  <p style="font-size:10.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:10.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
 <tr>
  <td width="51%" colspan="4" valign="top" style="padding:0in .7pt 0in .7pt;width:51.92%;">
  <p style="font-size:10.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:10.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
 <tr>
  <td width="51%" colspan="4" valign="top" style="padding:0in .7pt 0in .7pt;width:51.92%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">SCHERING-PLOUGH,
  LTD.</font></p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
 <tr>
  <td width="3%" valign="top" style="padding:0in .7pt 0in .7pt;width:3.62%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">By:</font></p>
  </td>
  <td width="38%" colspan="2" valign="top" style="border:none;border-bottom:solid windowtext .5pt;padding:0in .7pt 0in .7pt;width:38.08%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">/s/ David
  Poorvin</font></p>
  </td>
  <td width="10%" valign="top" style="padding:0in .7pt 0in .7pt;width:10.2%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
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  <td width="3%" valign="top" style="padding:0in .7pt 0in .7pt;width:3.62%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.28%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">DAVID
  POORVIN, PH.D.</font></p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
 </tr>
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  <td width="3%" valign="top" style="padding:0in .7pt 0in .7pt;width:3.62%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.28%;">
  <p style="margin:0in 0in .0001pt;"><font size="2" face="Times New Roman" style="font-size:10.0pt;">Prokurist</font></p>
  </td>
  <td width="48%" colspan="3" valign="top" style="padding:0in .7pt 0in .7pt;width:48.08%;">
  <p style="font-size:1.0pt;margin:0in 0in .0001pt;">&nbsp;</p>
  </td>
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