Amendment No. 1 to Third Amended and Restated Investor Rights Agreement



 Exhibit 10.4 

AMENDMENT NO. 1 TO THIRD AMENDED AND RESTATED INVESTOR RIGHTS AGREEMENT 

This Amendment No. 1 (the “Amendment”) to Third Amended and Restated Investor Rights Agreement is made
as of this 20th day of August, 2010, by and among
Achillion Pharmaceuticals, Inc. (the “Company”), and certain holders of the Company’s common stock, $.001 par value per share (the “Holders”), who are parties to the Third Amended and Restated Investor Rights Agreement,
dated as of August 11, 2008 (the “IRA”). 
 WHEREAS, the Company wishes to terminate several provisions of the
IRA; and 
 WHEREAS, the parties hereto wish to facilitate the termination but provide for certain rights as set forth herein to
survive such termination. 
 NOW, THEREFORE, in consideration of the mutual covenants herein contained and other valuable
consideration, the receipt and sufficiency of which is hereby acknowledged, the Company and the undersigned, who represent holders of at least two-thirds of the Conversion Shares (as defined in the IRA) held by the Holders, hereby agree as
follows: 
  

	1.	The definition of “Registration Rights Agreement” in Section 1 of the IRA is hereby deleted in its entirety and the following is inserted in lieu
thereof: 

 ““Registration Rights Agreement” means that certain Registration Rights Agreement,
dated on or about August 18, 2010, by and among the Company and the parties named therein (the “Purchasers”).” 
  

	2.	The following definition is hereby added to Section 1 of the Agreement: 


““Effective Date” means the date all of the Registrable Securities (as defined in the Registration Rights Agreement) have
been registered pursuant to effective registration statements filed pursuant to the Registration Right Agreement.”” 
  

	3.	Sections 4, 5, 10 and 11 of the IRA are hereby deleted in their entirety and shall have no further force or effect. 


 

	4.	Section 14(f) of the Agreement is hereby deleted in its entirety and the following is inserted in lieu thereof: 


“(f) The Company shall have no obligations pursuant to Section 6 with respect to any request or requests for registration made
by any Holder after October 25, 2013.” 
  

	5.	Section 14(h) of the Agreement is hereby deleted in its entirety and the following is inserted in lieu thereof: 


“(h) Notwithstanding anything to the contrary set forth in this Agreement, a Holder shall cease to be a Holder for purposes of this
Agreement when such Holder no longer holds Restricted Stock.” 








	6.	Any references to Sections 4 or 5 of the IRA are hereby deleted from the IRA. 


 

	7.	The Company represents and warrants to each Holder as follows: 


(i) The execution, delivery and performance of this Amendment by the Company have been duly authorized by all requisite corporate action
and will not violate any provision of law, any order of any court or other agency of government, the Charter or By-laws of the Company or any provision of any indenture, agreement or other instrument to which it or any of its properties or assets is
bound, conflict with, result in a breach of or constitute (with due notice or lapse of time or both) a default under any such indenture, agreement or other instrument or result in the creation or imposition of any lien, charge or encumbrance of any
nature whatsoever upon any of the properties or assets of the Company. 
 (ii) This Amendment has been duly executed and
delivered by the Company and constitutes the legal, valid and binding obligation of the Company, enforceable in accordance with its terms, subject to (A) laws of general application relating to bankruptcy, insolvency and the relief of debtors
and (B) rules of law governing specific performance, injunctive relief or other equitable remedies. 
  

	8.	Except as amended hereby, the IRA shall remain in full force and effect. 

  

	9.	This Amendment shall be governed by, and construed in accordance with, the laws of the State of Delaware, without regard to principles of conflicts of laws.


  

	10.	This Amendment may be executed in one or more counterparts, each of which shall be deemed to be an original and all of which shall constitute the same document.


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 IN WITNESS WHEREOF, the parties hereto have executed this Amendment as of the day and year
first above written. 
  

							
	ACHILLION PHARMACEUTICALS, INC.	 		 	
				
	By:	 	 /s/ Michael D. Kishbauch
	 		 	
	Name:	 	Michael D. Kishbauch	 		 	
	Title:	 	President and Chief Executive Officer	 		 	

  

			
	 Address:
	    	300 George Street
		    	New Haven, CT 06511

  

							
	HOLDERS:	 	
		
	 ADVENT HEALTH CARE & LIFE

SCIENCES II LIMITED PARTNERSHIP
	 	
				
	By:	 	 Advent International Limited Partnership,

General Partner
	 		 	
				
	By:	 	Advent International Corporation,	 		 	
		 	General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	
	Name:	 	Jason Fisherman	 		 	Dated: August 20, 2010
	Title:	 	Attorney-in-Fact	 		 	
			
	 ADVENT HEALTH CARE AND LIFE

SCIENCES II BETEILIGUNG GMBH & CO. KG
	 		 	
				
	By:	 	 Advent International Limited Partnership,

General Partner
	 		 	
				
	By:	 	Advent International Corporation,	 		 	
		 	General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-Fact	 		 	
		 		 		 	Dated: August 20, 2010









							
	ADVENT PARTNERS HLS II LIMITED PARTNERSHIP	 		 	
				
	By:	 	Advent International Corporation, General Partner	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	Dated: August 20, 2010
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-Fact	 		 	
			
	ADVENT PARTNERS LIMITED PARTNERSHIP	 		 	
				
	By:	 	 Advent International Corporation,

General Partner
	 		 	
				
	By:	 	 /s/ Jason Fisherman
	 		 	Dated: August 20, 2010
	Name:	 	Jason Fisherman	 		 	
	Title:	 	Attorney-in-fact	 		 	
			
	  
	 		 	Dated: August    , 2010
	Jonas V. Alsenas	 		 	
			
	ATLAS VENTURE ENTREPRENEURS’ FUND V, L.P.	 		 	
	ATLAS VENTURE FUND V, L.P.	 		 	
	ATLAS VENTURE PARALLEL FUND V-A, C.V.	 		 	
				
	By:	 	 Atlas Venture Associates V, L.P., their

General Partner
	 		 	
				
	By:	 	 Atlas Venture Associates V, Inc., its

General Partner
	 		 	
				
	By:	 	 /s/ Jean-Francois Formela
	 		 	
	Name:	 	Jean-Francois Formela	 		 	
	Title:	 	Vice President	 		 	
		 		 		 	Dated: August 20, 2010
			
	 BEAR STEARNS HEALTH

INNOVENTURES EMPLOYEE FUND, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	









							
	 BEAR STEARNS HEALTH INNOVENTURES

OFFSHORE, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	BEAR STEARNS HEALTH INNOVENTURES, L.P.	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 BSHI MEMBERS, L.L.C.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 BX, L.P.
	 		 	
				
	By:	 	 /s/ Todd Hesse
	 		 	Dated: August 20, 2010
	Name:	 	Todd Hesse	 		 	
	Title:	 	Managing Director on Behalf of the General Partner	 		 	
			
	 CAPITAL VENTURES INTERNATIONAL
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	 COMMUNITY INVESTMENT PARTNERS IV L.P., LLLP
	 		 	
				
	By:	 	 CIP Management L.P., LLLP, its managing

general partner
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	









							
	CONNECTICUT EMERGING ENTERPRISES, L.P.	 		 	
				
	By:	 	Emerging Enterprises Management LLC, its General Partner	 		 	
				
	By:	 	Connecticut Innovations, Incorporated, its Sole Member	 		 	
				
	By:	 	 /s/ Peter Longo
	 		 	Dated: August 20, 2010
	Name:	 	Peter Longo	 		 	
	Title:	 	President & Executive Director	 		 	
			
	CONNECTICUT INNOVATIONS, INCORPORATED	 		 	
				
	By:	 	 /s/ Peter Longo
	 		 	Dated: August 20, 2010
	Name:	 	Peter Longo	 		 	
	Title:	 	President & Executive Director	 		 	
			
	CRESTWOOD CAPITAL MASTER FUND LTD.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	CRESTWOOD CAPITAL PARTNERS II, L.P.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	  
	 		 	Dated: August    , 2010
	Kim Fennebresque	 		 	
			
	GE CAPITAL CORPORATION	 		 	
				
	By:	 	 /s/ Scott R. Towers
	 		 	Dated: August 20, 2010
	Name:	 	Scott R. Towers	 		 	
	Title:	 	Duly Authorized Signatory	 		 	









							
	GILEAD SCIENCES, INC.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	H&D INVESTMENTS 2001	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	INTERNATIONAL BIOTECHNOLOGY TRUST PLC.	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	KBL HEALTHCARE, L.P.	 		 	
				
	By:	 	 /s/ Marlene Krauss
	 		 	Dated: August 20, 2010
	Name:	 	Marlene Krauss	 		 	
	Title:	 	Managing Director	 		 	
			
	KBL PARTNERSHIP, L.P.	 		 	
				
	By:	 	 /s/ Marlene Krauss
	 		 	Dated: August 20, 2010
	Name:	 	Marlene Krauss	 		 	
	Title:	 	Managing Director	 		 	
			
	  
	 		 	Dated: August    , 2010
	David M. Malcolm	 		 	
			
	OAK INVESTMENT PARTNERS VIII, LIMITED PARTNERSHIP	 		 	
				
	By:	 	Oak Associates VIII, LLC, its General Partner	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
		 	            A Member	 		 	









							
	OAK VIII AFFILIATES FUND , LIMITED PARTNERSHIP	 		 	
				
	By:	 	Oak Associates VIII, LLC, its General Partner	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
		 	        A Member	 		 	
			
	OAKWOOD MEDICAL INVESTORS III (QP), L.L.C.	 		 	
				
	By:	 	 Oakwood Medical Management III, L.L.C.,

its Manager
	 		 	
				
	By:	 	 /s/ Raul E. Perez
	 		 	Dated: August 20, 2010
	Name:	 	Raul E. Perez, M.D.	 		 	
	Title:	 	President	 		 	
			
	OAKWOOD MEDICAL INVESTORS III, L.L.C.	 		 	
				
	By:	 	 Oakwood Medical Management III, L.L.C.,

its Manager
	 		 	
				
	By:	 	 /s/ Raul E. Perez
	 		 	Dated: August 20, 2010
	Name:	 	Raul E. Perez, M.D.	 		 	
	Title:	 	President	 		 	
			
	  
	 		 	Dated: August    , 2010
	Stelios Papadopoulos	 		 	
			
	PGE INVESTMENTS 2002, LLC	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	  
	 		 	Dated: August    , 2010
	Barbara A. Piette	 		 	
			
	POUND CAPITAL CORPORATION	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	

  








							
	  
	 		 	Dated: August    , 2010
	Peter Reikes	 		 	
			
	SCHEER INVESTMENT HOLDINGS III, LLC	 		 	
				
	By:	 	 /s/ David I. Scheer
	 		 	Dated: August 20, 2010
	Name:	 	David I. Scheer	 		 	
	Title:	 	Managing Member	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II GROUP CO-INVESTMENT SCHEME
	 		 	
				
	By:	 	SITCO Nominees Ltd. – VC 01903, its Nominee	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II LP1
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	SCHRODER VENTURES INTERNATIONAL LIFE SCIENCES FUND II LP2	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	

  








							
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II LP3
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	 SCHRODER VENTURES INTERNATIONAL LIFE

SCIENCES FUND II STRATEGIC PARTNERS L.P.
	 		 	
				
	By:	 	Schroder Venture Managers Inc., its General Partner	 		 	
				
	By:	 	 /s/ Lana Desmond        /s/ Donna Douglas
	 		 	Dated: August 20, 2010
	Name:	 	Lana Desmond                  Donna Douglas	 		 	
	Title:	 	Authorized Signatures	 		 	
			
	SCHRODER VENTURES INVESTMENTS LIMITED	 		 	
				
	By:	 	SV (Nominees) Limited, its Nominee	 		 	
				
	By:	 	 /s/ John Marren
	 		 	Dated: August 20, 2010
	Name:	 	John Marren	 		 	
	Title:	 	Director	 		 	
			
	SG VENTURES I, L.P.	 		 	
				
	By:	 	 Société Générale Investment Corporation,

its General Partner
	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title:	 		 		 	
			
	TRINITY EQUITY INVESTMENTS I, LLC	 		 	
				
	By:	 	 /s/ Sengal Selassie
	 		 	Dated: August 20, 2010
	Name:	 	Sengal Selassie	 		 	
	Title:	 	President	 		 	









							
	WEBSTER FINANCIAL CORPORATION	 		 	
				
	By:	 	 /s/ Joseph Savage
	 		 	Dated: August 20, 2010
	Name:	 	Joseph Savage	 		 	
	Title:	 	EVP – Commercial Banking	 		 	
			
	  
	 		 	Dated: August    , 2010
	Christopher White	 		 	
			
	YALE UNIVERSITY	 		 	
				
	By:	 	  
	 		 	Dated: August    , 2010
	Name:	 		 		 	
	Title: