Exhibit
10.1


AMENDMENT NO. 1


This Amendment No. 1 (this “Amendment No. 1”) is to
the Collaboration and License Agreements, effective as of July 9, 2003, between
(i) Pharmacopeia Drug Discovery, Inc. (f/k/a Pharmacopeia, Inc.) and Schering
Corporation and (ii) Pharmacopeia Drug Discovery, Inc. and Schering-Plough Ltd.
(collectively, the “2003 Agreements”). By agreement of the Parties, as of the
Amendment No.1 Effective Date (as defined below), this Amendment No.1 amends
the 2003 Agreements as follows:


1.             All
capitalized terms not defined in this Amendment No. 1 shall have the


meanings given to them in
the 2003 Agreements.


2.             The
Parties agree that this Amendment No. 1 is effective as of June 10, 2006 (the “Amendment
No. 1 Effective Date”).


3.             The
Parties agree that as of the Amendment No. 1 Effective Date, and
notwithstanding anything in the 2003 Agreements to the contrary:


(a)                                   The
term of the Collaboration is extended and shall continue until October 7, 2006, on which date it shall
terminate.


(b)                                  For
the period from June 10, 2006 until October 7, 2006, Pharmacopeia shall provide ten (10) chemistry FTEs for
the performance of the Collaboration. During such period, each of Schering and
SPL shall pay to Pharmacopeia research funding for the Collaboration at the rate
per FTE established for the third year of the Collaboration pursuant to
Sections 5.2.2 of the
Agreements. All such FTEs shall be dedicated to work full time on the
Collaboration.


(c)                                   Subject
to Section 4 below, the FTEs that Pharmacopeia provides under Section 3(b)
above shall work on Optimization Programs designated by the Collaboration
Committee. For the avoidance of doubt, such FTEs shall not be required to work
on Screening Programs.


(d)                                  Payments
by each of Schering and SPL under Section 3(b) above shall be made to
Pharmacopeia in accordance with Section 5.2.3
of the 2003 Agreements.


4.             The
Parties agree that Pharmacopeia will not initiate or perform any new
Optimization Programs under the 2003 Agreements
during the period set forth in Section
3(b) above.


5.             The remaining terms of the 2003 Agreements,
except to the extent modified by the terms of this Amendment No. 1, shall
remain in full force and effect.









 



IN WITNESS WHEREOF, the parties hereto have caused
this Amendment No. 1 to be duly executed by their authorized representatives
and delivered in triplicate originals.




	
  SCHERING CORPORATION

  	
   

  	
  PHARMACOPEIA DRUG DISCOVERY,

  
	
   

  	
   

  	
   

  	
   

  	
  INC. (F/K/A PHARMACOPEIA, INC.)

  
	
   

  	
   

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  
	
  By:

  	
   

  	
  /s/ Michael J. DuBois_

  	
   

  	
   

  	
   

  	
   

  
	
  Name:

  	
   

  	
  Michael J. DuBois

  	
   

  	
  By:

  	
   

  	
  /s/ Leslie J. Browne, Ph. D.

  
	
  Title:

  	
   

  	
  Vice President

  	
   

  	
  Name:

  	
   

  	
  Leslie J. Browne, Ph.D.

  
	
   

  	
   

  	
   

  	
   

  	
  Title:

  	
   

  	
  President and Chief Executive Officer

  
	
   

  	
   

  	
   

  	
   

  	
  Date:

  	
   

  	
  July 27, 2006

  
	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  	
   

  
	
  SCHERING-PLOUGH, LTD.

  	
   

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  	
   

  	
   

  
	
  By:

  	
   

  	
  /s/ Michael J. DuBois

  	
   

  	
   

  	
   

  	
   

  
	
  Name:

  	
   

  	
  Michael J. DuBois

  	
   

  	
   

  	
   

  	
   

  
	
  Title:

  	
   

  	
  Officer

  	
   

  	
   

  	
   

  	
   

  






 



 2