exv4w1



 





Exhibit 4.1





AMENDMENT NO. 3

TO

RIGHTS AGREEMENT




          This AMENDMENT NO. 3 TO RIGHTS AGREEMENT (the “Amendment”) is entered into as of January 16,
2007, between Idera Pharmaceuticals, Inc., a Delaware corporation (the “Company”), and Mellon
Investor Services LLC, a New Jersey limited liability company, as Rights Agent (the “Rights
Agent”). Capitalized terms not otherwise defined herein shall have the meanings given them in the
Rights Agreement, dated as of December 10, 2001, as amended (the “Rights Agreement”), between the
parties hereto.



RECITALS



WHEREAS, the Board has previously determined that it was in the best interest of the Company to
amend, and the Company did so amend, the Rights Agreement to modify the definition of Exempted
Person to exclude a certain stockholder of the Company from such definition in specified
circumstances;



WHEREAS, the Board has determined that it is in the best interest of the Company to further modify
such definition of Exempted Person to increase the number of shares such stockholder may hold;



WHEREAS, the address of the General Counsel of the Rights Agent has changed; and



WHEREAS, the Company has determined that the Rights Agreement be amended in accordance with Section
27 of the Rights Agreement, as set forth herein, and the Rights Agent is hereby directed to join in
the amendment to the Rights Agreement as set forth herein.




AGREEMENT



NOW THEREFORE, the parties hereto, intending to be legally bound, hereby agree as follows:



1.        Section 1(oo) of the Rights Agreement is hereby amended to read in its entirety as follows:





	 	 	“(oo) 	“Exempted Person” shall mean Baker Brothers Investments, together with all of
its Affiliates and Associates (“Baker Brothers”), unless and until such time as Baker
Brothers, directly or indirectly, becomes the Beneficial Owner of more than 5,375,000
shares (subject to appropriate adjustment to reflect any stock split, reverse stock
split, stock dividend, combination, reclassification or other similar recapitalization
affecting such shares) of the Common Stock (disregarding for purposes of this
calculation any shares of Common Stock purchased by Baker Brothers pursuant to the
participation right (the “Participation Right”) set forth in Section 5.2 of that
certain Common Stock Purchase Agreement, dated March 24, 2006, by and among the Company
and the purchasers listed in Exhibit A thereto (the “CSP Agreement”)). Notwithstanding
the preceding sentence, if following the date on which its Participation Right
terminates in accordance with the CSP Agreement, Baker Brothers, directly or
indirectly, is or becomes the Beneficial




 









 






	 	 	 	Owner of less than 14% of the Common Stock then outstanding, Baker Brothers
immediately shall cease to be an Exempted Person. The Company acknowledges that the
Rights Agent has no knowledge of the CSP Agreement.”




2.        The second paragraph of Section 26 of the Rights Agreement is hereby amended to read as follows:





	 	 	 	“Subject to the provisions of Section 21, any notice or demand authorized by this
Agreement to be given or made by the Company or by the holder of any Rights
Certificate to or on the Rights Agent shall be sufficiently given or made if sent by
first-class mail, postage prepaid, addressed (until another address is filed in
writing with the Company) or by facsimile transmission as follows as follows:





	 	 	 
	 

	 	Mellon Investor Services LLC
	 

	 	111 Founder’s Plaza 11th Floor
	 

	 	East Hartford, CT 06108
	 

	 	Attention: Relationship Manager
	 

	 	Facsimile No.: (860) 528-6472
	 
	 	 
	 

	 	with a copy to:
	 
	 	 
	 

	 	Mellon Investor Services LLC
	 

	 	480 Washington Boulevard
	 

	 	Jersey City, NJ 07310
	 

	 	Attention: General Counsel
	 

	 	Facsimile No.: (201) 680-4610”






3.        Except as amended hereby, the Rights Agreement shall remain unchanged and shall remain in full
force and effect.



4.        This Amendment may be executed in any number of counterparts, each of which shall be an
original, but all of which together shall constitute one instrument.



5.        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 Delaware
applicable to contracts made and to be performed entirely within Delaware; provided, however, that
all rights, duties and obligations of the Rights Agent shall be governed by and construed in
accordance with the laws of the State of New York applicable to contracts made and to be performed
entirely within such state.



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IN WITNESS WHEREOF, the parties have caused this Amendment to be executed by their respective duly
authorized representatives as of the date first above written.




	 	 	 	 	 
	IDERA PHARMACEUTICALS, INC.

 	 	 
	By:  	/s/ SUDHIR AGRAWAL
 	 	 
	 	Name:  	Sudhir Agrawal 	 	 
	 	Title:  	Chief Executive Officer 	 	 
	 



	 	 	 	 	 
	MELLON INVESTORS SERVICES LLC,

as Rights Agent

 	 	 
	By:  	/s/ JOHN J. BORYCZKI
 	 	 
	 	Name:  	John J. Boryczki 	 	 
	 	Title:  	Client Relationship Executive