Exhibit 4.1


AMENDMENT TO


RIGHTS AGREEMENT


THIS AMENDMENT TO RIGHTS
AGREEMENT (the “Amendment”),
dated as of July 5th,
2007, between TAPESTRY
PHARMACEUTICALS, INC., a Delaware corporation (the “Company”), and AMERICAN STOCK TRANSFER & TRUST COMPANY (the “Rights Agent”).


WHEREAS, the
Company and the Rights Agent have previously entered into that certain Rights
Agreement, dated as of December 12, 2006 (the “Agreement”);


WHEREAS,
Section 27 of the Agreement provides that prior to the Distribution Date (such
term, and all other capitalized terms used but not defined herein, shall have
the meaning assigned thereto in the Agreement), the Company and the Rights
Agent shall, if the Company so directs, supplement or amend any provision of
the Agreement without the approval of any holders of the Rights;


WHEREAS, the
Company desires to amend the definition of “Excluded Stockholder” contained in
the Agreement to narrow such definition so as to exclude from an exception for
acquisitions that will not result in such Person becoming an Acquiring Person
certain acquisitions of shares pursuant to that certain Purchase Agreement,
dated as of February 2, 2006, by and among the Company and the other parties
thereto or upon the exercise of certain warrants issued under such Purchase
Agreement and to reflect the acquisition of certain Common Shares and warrants
to acquire Common Shares by certain Excluded Stockholders;


WHEREAS, the
Company desires to amend the Agreement such that a “Distribution Date” does not
occur until ten days after the Shares Acquisition Date; and


WHEREAS, this
Amendment is in compliance with the terms of Section 27 of the Agreement and
will not adversely affect the interest of the Rights Agent under this
Agreement.


Accordingly, in consideration of the premises and the
mutual agreements herein set forth, the parties hereby agree as follows:


SECTION 1.                       AMENDMENTS.


(a)                               The
definition of “Excluded Stockholder” contained in Section 1(h) of the Agreement
is hereby amended and restated in its entirety as follows:


“Excluded
Stockholder” shall mean any of the following Persons:  Special Situations Fund III QP, L.P., Special
Situations Fund III, L.P., Special Situations Cayman Fund, L.P., Special
Situations Private Equity Fund, L.P., Special Situations Life Sciences Fund,
L.P., Baker Brother Life Sciences Fund, L.P., 14159, L.P., Biotechnology Value
Fund II, L.P., BVF Investments, L.L.C., Investment 10, L.L.C., Fort Mason
Master, L.P., Fort Mason Partners, L.P., Tang Capital Partners, LP, Kevin C.
Tang as Custodian for Julian Kong Tang Under the CA Transfer to Minors Act,
Kevin C. Tang as Custodian for Justin Lee Tang Under the CA Transfer to Minors
Act, Kevin C. Tang as Custodian for Noa













Young Tang Under the CA
Transfer to Minors Act, Kevin Tang and Haeyoung Tang Trustees The Tang Family
Trust Dated 8-27-02, IRA FBO Kevin Tang DB Securities Inc. Custodian Rollover
Account and any Person whose beneficial ownership of Common Shares is by or
through any of such Persons; provided that
any such Person shall not be an Excluded Stockholder in the event that such
Person, together with all Affiliates and Associates of such Person, acquires in
the aggregate (together with all other acquisitions of Common Shares by such
Person and all Affiliates and Associates of such Person pursuant to this
proviso, but excluding any Common Shares acquired by such Person pursuant to
the terms of that certain Purchase Agreement, dated as of February 2, 2006, by
and among the Company and the other parties thereto or pursuant to the terms of
warrants issued to such Person under such Purchase Agreement and excluding, in
the case of Special Situations Fund III QP, L.P., Special Situations Fund III,
L.P., Special Situations Cayman Fund, L.P., Special Situations Private Equity
Fund, L.P., Special Situations Life Sciences Fund, L.P., 709,832 Common Shares acquired from Versant Capital
Management LLC and 750,000 Common Shares issuable upon exercise of a warrant
originally issued under such Purchase Agreement to Versant Capital Management
LLC) more than 1.0% of the then issued and outstanding Common Shares after
April 4, 2006.


(b)          The first sentence of Section 3(a) of the Agreement is hereby
amended and restated in its entirety as follows:


Until the earlier of the
Close of Business on (i) the tenth day after the Shares Acquisition Date or
(ii) the tenth Business Day (or such later date as may be determined by action
of the Board of Directors prior to such time as any Person becomes an Acquiring
Person) after the date of the commencement (determined in accordance with Rule
14d-2 under the Exchange Act) by any Person (other than the Company, any
Subsidiary of the Company, any employee benefit plan of the Company or of any
Subsidiary of the Company or any entity holding Common Shares for or pursuant
to the terms of any such plan) of, or of the first public announcement of the
intention of any Person (other than the Company, any Subsidiary of the Company,
any employee benefit plan of the Company or of any Subsidiary of the Company or
any entity holding Common Shares for or pursuant to the terms of any such plan)
to commence, a tender or exchange offer (which intention to commence remains in
effect for five Business Days after such announcement), the consummation of
which would result in any Person becoming an Acquiring Person (including any
such date which is after the date of this Agreement and prior to the issuance
of the Rights, the earlier of such dates being herein referred to as the “Distribution Date”),
(x) the Rights will be evidenced by the certificates for Common Shares
registered in the names of the holders thereof (which certificates shall also
be deemed to be Right Certificates) and not by separate Right Certificates, and
(y) the Rights (and the right to receive Right Certificates therefor) will be
transferable only in connection with the transfer of Common Shares.



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SECTION 2.        EFFECT OF AMENDMENT.  Except
as expressly set forth in Section 1, the Agreement shall remain unchanged and
continue in full force and effect.


SECTION 3.        GOVERNING LAW. 
This Amendment shall be deemed to be a contract made under the laws of
the State of Delaware and for all purposes shall be governed by and construed
in accordance with the laws of such State applicable to contracts to be made
and performed entirely within such State.


SECTION 4.        COUNTERPARTS. 
This Amendment may be executed in any number of counterparts and each of
such counterparts shall for all purposes be deemed to be an original, and all
such counterparts shall together constitute but one and the same instrument.


SECTION 5.        DESCRIPTIVE HEADINGS. 
Descriptive headings of the several Sections of this Amendment are
inserted for convenience only and shall not control or affect the meaning or
construction of any of the provisions hereof.


[Signatures
follow]



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IN
WITNESS WHEREOF, parties whereto have caused this Amendment
to be duly executed, all as of the day and year first above written.


	
  Attest:

  	
   

  	
  TAPESTRY PHARMACEUTICALS, INC. 

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  /s/ JANE C. SCHATZ

  	
   

  	
   

  	
  /s/ GORDON H.
  LINK, JR.

  	
   

  
	
  Name: Jane C.
  Schatz

  	
   

  	
  Name: Gordon H. Link, Jr.

  
	
  Title: Corporate
  Paralegal

  	
   

  	
  Title: Senior Vice President and Chief Financial
  Officer

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  Attest:

  	
   

  	
  AMERICAN STOCK TRANSFER & TRUST

  COMPANY

  
	
   

  	
   

  	
   

  
	
   

  	
   

  	
   

  
	
  /s/ WENDY CAPPIELLO

  	
   

  	
   

  	
  /s/ HERBERT J.
  LEMMER

  	
   

  
	
  Name: Wendy
  Cappiello

  	
   

  	
  Name: Herbert J. Lemmer

  
	
  Title: Associate

  	
   

  	
  Title: Vice President

  



 



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