Exhibit 4.1


 


DISCOVERY
PARTNERS INTERNATIONAL, INC.


 


FIRST
AMENDMENT TO RIGHTS AGREEMENT


 


THIS FIRST AMENDMENT TO RIGHTS AGREEMENT
(this “Amendment”) is made as of April
10, 2006 between DISCOVERY PARTNERS INTERNATIONAL, INC., a
Delaware corporation (the “Company”),
and AMERICAN STOCK TRANSFER & TRUST COMPANY, as
rights agent (the “Rights
Agent”).


 


WHEREAS, the Company and the
Rights Agent entered into that certain Rights Agreement dated as of February 13,
2003 (the “Rights Agreement”)
(capitalized terms used but not defined herein shall have the meaning assigned
to them in the Rights Agreement); and


 


WHEREAS, the Company and the
Rights Agent desire to irrevocably amend the Rights Agreement as provided
below.


 


NOW, THEREFORE, in consideration
of the foregoing premises and the mutual covenants and conditions set forth
below, and for other good and valuable consideration, the receipt of which is
hereby acknowledged, the parties to this First Amendment to Rights Agreement
hereby agree as follows:


 


AMENDMENT


 


1.                                      Amendment
of the Rights Agreement.


 


1.1          A new Section 35 of
the Rights Agreement is hereby added as follows:


 


“Section 35. Permitted Transactions. Reference
is made to (a) the Agreement and Plan of Merger and Reorganization by and among
the Company, Infinity Pharmaceuticals, Inc., a Delaware corporation (“Infinity”), and Darwin Corp., a
wholly-owned corporate subsidiary of the Company organized under Delaware law (“Merger Sub”), to be dated as of a
date occurring on or after April 10, 2006 and on or before April 14, 2006 (such
date, the “Execution Date”), as it may
be amended from time to time (the “Merger Agreement”)
and (b) the Voting Agreements by and between the Company and certain
stockholders of Infinity, to be dated as of the Effective Date, as each may be
amended from time to time (the “Voting Agreements”).
Notwithstanding any other provision of this Agreement, the term “Acquiring
Person” as used throughout this Agreement shall not include the stockholders of
Infinity, or any of such stockholder’s Affiliates or Associates, in each case
to the extent, but only to the extent, that any such stockholder or any of such
Affiliates or Associates, becomes or shall become the Beneficial Owner of 15%
or more of the shares of Common Stock of the Company then outstanding as a
result of the execution, delivery or performance of the Merger Agreement or the
Voting Agreements (or any of them) or the consummation of the Merger (as such
term is defined in the Merger Agreement) or the transactions contemplated
thereby, in each case in accordance with the terms thereof, as such terms may
be amended by the parties thereto. In addition, notwithstanding any other
provision


 


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of this Agreement, neither a Distribution Date nor a Share
Acquisition Date shall be deemed to occur, and the Rights will not separate
from the Common Stock, as a result of the execution, delivery or performance of
the Merger Agreement or the Voting Agreements (or any of them) or the
consummation of the Merger (as such term is defined in the Merger Agreement) or
the transactions contemplated thereby, in accordance with the terms thereof, as
such terms may be amended by the parties thereto.”


 


2.             No Other Amendment.
Except as modified by this Amendment, the Rights Agreement shall remain in full
force and effect without any modification. By executing this Amendment below,
the Company certifies that this Amendment has been executed and delivered in
compliance with the terms of Section 27 of the Rights Agreement. This Amendment
shall be deemed an amendment to the Rights Agreement and shall become effective
when executed and delivered by the Company and the Rights Agent as provided
under Section 27 of the Rights Agreement. This Amendment shall be irrevocable.


 


3.             Counterparts.  This Amendment may be
executed in several counterparts, each of which shall constitute an original
and all of which, when taken together, shall constitute one agreement.


 


 


[THIS SPACE INTENTIONALLY LEFT BLANK]


 


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The foregoing
Amendment is hereby executed as of the date first above written.


 


THE COMPANY:


 


DISCOVERY PARTNERS INTERNATIONAL, INC.


 


 


	
  By:

  	
  /s/ Michael C. Venuti

  	
   

  
	
   

  	
  Michael C. Venuti

  
	
   

  	
  Acting Chief Executive Officer

  
	
   

  
	
   

  
	
  RIGHTS AGENT:

  
	
   

  
	
  AMERICAN STOCK TRANSFER & TRUST COMPANY

  
	
   

  
	
   

  
	
  By:

  	
  /s/ Herbert J. Lemmer

  	
   

  
	
  Name:

  	
  Herbert J. Lemmer

  	
   

  
	
  Title:

  	
  Vice President

  	
   

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  By:

  	
   

  	
   

  	 

	
  Name:

  	
   

  	
   

  
	
  Title: