**Exhibit 10.31**

 

* CERTAIN INFORMATION IN THIS EXHIBIT HAS BEEN OMITTED AND FILEDSEPARATELY WITH THE COMMISSION. CONFIDENTIAL TREATMENT HAS BEEN REQUESTED WITHRESPECT TO THE OMITTED PORTIONS. 

 

**AMENDMENT NO. 5**

 

This AmendmentNo. 5 (this “Amendment No. 5”) to the Collaboration and License Agreementseffective October 29, 1998 between the parties hereto, as amended previously(the “1998 Agreements”), is effective as of July 9, 2003 (the “Amendment No. 5Effective Date”) and by agreement of the parties as of the Amendment No. 5Effective Date amends the 1998 Agreements as follows:

 

1.             All capitalized termsherein shall have the same meaning as in the 1998 Agreements.

 

2.             The parties agreethat as of the Amendment No. 5 Effective Date:

 

(i)            Schering’s and SPL’sexclusivity with respect to *;

 

(ii)           The Exclusivity Periodswith respect to *;

 

(iii)          *

 

(iv)          Subject to theprovisions of Section 4.5 of the 1998 Agreements, *

 

3.             Section 5.2.4 of each1998 Agreement is hereby amended by adding to the end of such Section of that1998 Agreement the following:

 

(a)           *

 

(b)           * Interim Period.Pharmacopeia agrees that, notwithstanding its right under the first sentence ofSection 5.2.4 (as previously amended) to remove FTEs from the Collaborationbeginning * it shall not exercise such right during the Interim Period. The“Interim Period,” as used herein, shall mean the period beginning *

 

(c)           Staffing and PaymentDuring Interim Period. During the Interim Period, (i) the parties agreethat Pharmacopeia shall provide, and each of Schering and SPL shall fund, *FTEs *, (ii) each of Schering and SPL shall pay Pharmacopeia for these * FTEsat the rate of * and (iii) all other provisions of the 1998 Agreements * shallremain in full force and effect in accordance with their respective terms. Forthe avoidance of doubt, it is understood and agreed by the parties that (A) foreach 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 *.

 

(d)           *

 

(B)           Extensionof Collaboration Term. Notwithstanding Section 2.2.1 of the 1998Agreements, the term of the Collaboration shall be extended until *.

 

(C)           *Collaboration. In lieu of its rights and the other terms provided underSection 5.2.4 of the 1998 Agreements (as in effect prior to the Amendment No. 5Effective Date), Pharmacopeia shall have the right, starting *, to remove FTEsfrom the Collaboration * such that the minimum number of Pharmacopeia FTEsassigned 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 theAmendment No. 5 Effective Date) for *. In the event that Schering or SPLrequests

 

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additionalPharmacopeia manpower be available to the Collaboration * (i.e., in addition tothe 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 *.”

 

(D)          Revocationof Section 2 of Amendment No. 5. All of the provisions set forth in Section2 of this Amendment No. 5 shall be revoked and of no force and effect as of theearlier of *

 

4.             The remaining termsof the 1998 Agreements, except to the extent modified by the terms of thisAmendment, the agreement letter dated March 29, 1999, Amendment No. 1 effectiveApril 15, 1999, Amendment No. 2 effective October 1, 1999, Amendment No. 3effective April 17, 2003 and Amendment No. 4 effective May 29, 2003, shallremain in full force and effect.

 

IN WITNESSWHEREOF, the parties hereto have caused this Amendment No. 5 to be dulyexecuted by their authorized representatives and delivered in triplicateoriginals on the Amendment No. 5 Effective Date.

 
| SCHERING  CORPORATION  | PHARMACOPEIA,  INC.   |
|------------------------|-----------------------|
| By:                    | /s/ David  Poorvin    |   | By: | /s/ Stephen  A. Spearman |   |
|                   | DAVID  POORVIN, PH.D. |   | STEPHEN A.  SPEARMAN, PH.D. |
|                   | Vice  President       |   | Executive  Vice President and  Chief Operating Officer |
|                   |                  |
|                   |                  |
| SCHERING-PLOUGH,  LTD. |                  |
| By:                    | /s/ David  Poorvin    |   |   |
|                   | DAVID  POORVIN, PH.D. |   |
|                   | Prokurist             |   |
|                        |                       |  |  |  |  |  |

 

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