Prepared by R.R. Donnelley Financial -- EX-4.4



 Exhibit 4.4 

CYMABAY THERAPEUTICS, INC. 

AMENDMENT NO. 1 TO REGISTRATION RIGHTS AGREEMENT 

This Amendment No. 1 (the “Amendment”) to that certain Registration Rights Agreement, dated as of
September 30, 2013 (the “Agreement”), is made as of October 30, 2013, by and among CymaBay Therapeutics, Inc., a Delaware corporation (the “Company”), and the undersigned Holders of at least
fifty percent (50%) of the outstanding Registrable Securities. All capitalized terms used but not otherwise defined herein shall have the meanings given them in the Agreement unless the context otherwise requires. 

RECITALS 

WHEREAS, the Company and the Holders desire to amend the Agreement as set forth below; and 

WHEREAS, to amend the Agreement, Section 6(g) of the Agreement requires the written consent
of the Company and the holders of at least fifty percent (50%) of the outstanding Registrable Securities. 

AGREEMENT 

NOW, THEREFORE, in consideration of the mutual promises, representations, warranties,
covenants and conditions set forth in the Agreement and this Amendment, the receipt and sufficiency of which is hereby acknowledged, the parties hereto hereby amend the Agreement as follows: 

1. The defined term “Filing Deadline” is hereby amended and restated in its entirety to read as follows: 

“Filing Deadline” means, with respect to the Registration Statement required to be filed pursuant to Section 2(a),
the 30th calendar day following October 31, 2013 and, provided, however, that if the Filing Deadline falls on a Saturday, Sunday or other day that the Commission is closed for business, the Filing Deadline shall be extended to the next Business
Day on which the Commission is open for business.” 
 2. Section 6(g) of the Agreement is hereby amended and restated
in its entirety to read as follows: 
 “Amendments and Waivers. The provisions of this Agreement, including the provisions of
this sentence, may not be amended, modified or supplemented unless the same shall be in writing and signed by the Company and Holders holding 50% of the then outstanding Registrable Securities, and waivers or consents to departures from the
provisions hereof may not be given, unless the same shall be in writing and signed by the Company and Holders holding 50% of the then outstanding Registrable Securities; provided however, that execution of a Joinder Agreement by additional
Purchasers after the Agreement Date shall not be deemed to be an amendment to this Agreement. For the avoidance of doubt, any Purchaser pursuant to the Institutional Purchase Agreement may become a party to this Agreement by executed a
Joinder Agreement on or before November 22, 2013, and be deemed a Purchaser and Holder for all purposes hereunder. If a Registration Statement does not register all of the Registrable Securities pursuant to a waiver or amendment done in
compliance with the previous sentence, then the number of Registrable Securities to be registered for each Holder shall be reduced pro rata among all Holders. Notwithstanding the foregoing, a waiver or consent to depart from the provisions hereof
with respect to a matter that relates exclusively to the rights of Holders and that does not directly or 







 
indirectly affect the rights of other Holders may be given by Holders of all of the Registrable Securities to which such waiver or consent relates; provided, however, that the provisions of this
sentence may not be amended, modified, or supplemented except in accordance with the provisions of the first sentence of this Section 6(g).” 

3. The Agreement, as amended by this Amendment, shall remain in full force and effect. 

4. This Amendment shall be governed by and construed under the laws of the State of New York as such laws are applied to agreements
among New York residents entered into and performed entirely within the State of New York. 
 5. This Amendment may be executed
simultaneously in multiple counterparts, each of which shall be deemed an original, but all of which taken together shall constitute one and the same instrument. Execution and delivery of this Amendment by exchange of facsimile copies bearing the
facsimile signature of a party hereto shall constitute a valid and binding execution and delivery of this Amendment by such party. Such facsimile copies shall constitute enforceable original documents. 

[Remainder of Page Intentionally Left Blank] 







 IN WITNESS WHEREOF, the parties have executed this Amendment No. 1 to Registration Rights
Agreement as of the date first written above. 
  

			
	CymaBay Therapeutics, Inc.
		
	By:	 	/s/ Harold VanWart
		 	Name: Harold Van Wart
		 	Title: Chief Executive Officer









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

					
	 ALTA BIOPHARMA PARTNERS III, L.P.

		 	By: Alta BioPharma Management III, LLC,
			
		 	By:	 	/s/ Ed Penhoet
		 		 	Name: Ed Penhoet
		 		 	Title: Director
	
	
ALTA BIOPHARMA PARTNERS III 
GMBH & CO.
 BETEILIGUNGS KG

		 	By: Alta BioPharma Management III, LLC
			
		 	By:	 	/s/ Ed Penhoet
		 		 	Name: Ed Penhoet
		 		 	Title: Director
	
	ALTA BIOPHARMA PARTNERS III, LLC
			
		 	By:	 	/s/ Ed Penhoet
		 		 	Name: Ed Penhoet
		 		 	Title: Director









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

					
	 VERSANT VENTURE CAPITAL II, L.P.

		
		 	By: Versant Ventures II, LLC
		 	Its: General Partner
			
		 	By:	 	/s/ Bradley J. Bolzon
		 		 	Name: Bradley J. Bolzon
		 		 	Title:   Managing Director
	
	 VERSANT SIDE FUND II, L.P.

		
		 	By: Versant Ventures II, LLC
		 	Its: General Partner
			
		 	By:	 	/s/ Bradley J. Bolzon
		 		 	Name: Bradley J. Bolzon
		 		 	Title:   Managing Director
	
	 VERSANT AFFILIATES FUND II-A, L.P.

		
		 	By: Versant Ventures II, LLC
		 	Its:  General Partner
			
		 	By:	 	/s/ Bradley J. Bolzon
		 		 	Name: Bradley J. Bolzon
		 		 	Title:   Managing Director









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

			
	
JOHNSON & JOHNSON 
DEVELOPMENT
 CORPORATION

		
	By:	 	/s/ Ashish K. Xavier


 
			
		
	Name:	 	Ashish K. Xavier


 
			
		
	 Title:
	 	VP, Venture Investments









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

			
	 DEERFIELD SPECIAL SITUATIONS FUND, L.P. 

	
	By: Deerfield MGMT, L.P.
	Its: General Partner
	 By: J.E. Flynn Capital, LLC

	 Its: General Partner

		
	By:	 	/s/ David J. Clark
		 	Name: David J. Clark
		 	Title: Authorized Signatory
	
	 DEERFIELD SPECIAL SITUATIONS
MASTER
 FUND, L.P. 

	
	By: Deerfield MGMT, L.P.
	Its: General Partner
	 By: J.E. Flynn Capital, LLC

	 Its: General Partner

		
	By:	 	/s/ David J. Clark
		 	Name: David J. Clark
		 	Title: Authorized Signatory









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

			
	 PICTET BIOTECH 

		
	By:	 	/s/ Marie-Claude Lange
	   /s/ Alexandre Ris

		 	Name: Marie-Claude Lange/Alexandre Ris
		 	Title: Directors









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

			
	 VENROCK PARTNERS, L.P. 

	
	 By: Venrock Partners Management, LLC

	 Its: General Partner

		
	By:	 	/s/ Anthony B. Evnin
		 	Name: Anthony B. Evnin
		 	Title:   Member
	
	 VENROCK ASSOCIATES IV, L.P. 

	
	 By: Venrock Management IV, LLC

	 Its: General Partner

		
	By:	 	/s/ Anthony B. Evnin
		 	Name: Anthony B. Evnin
		 	Title:   Member
	
	VENROCK ENTREPRENEURS FUND IV, L.P. 
	
	 By: VEF Management IV, LLC

	Its: General Partner
		
	By:	 	/s/ Anthony B. Evnin
		 	Name: Anthony B. Evnin
		 	Title:   Member









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

					
	 T. ROWE PRICE HEALTH SCIENCES FUND,
INC. 

		
		 	By: T.Rowe Price Associates, Inc.,
	Investment Adviser
			
		 	By:	 	/s/ Taymour Tamaddon
		 	  Name: Taymour Tamaddon
		 	  Title: Vice President









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

					
	 ALLIANCEBERNSTEIN VENTURE FUND I, L.P.

	By: AllianceBernstein ESG Venture
	Management, L.P., its General Partner
	By: AllianceBernstein Global Derivatives
	Corporation, its General Partner
			
		 	By:	 	/s/ Troy Fukumoto
		 		 	Name: Troy Fukumoto
		 		 	Title: Vice President









 JOINDER AGREEMENT 

For good and valuable consideration, the receipt and sufficiency of which is hereby acknowledged, and intending to be legally bound, the
undersigned hereby acknowledges receipt of a true and complete copy of the Amendment No. 1 to Registration Rights Agreement, dated as of October 30, 2013, by and among CymaBay Therapeutics, Inc. and the Purchasers party thereto, and agrees
to be bound by all of the provisions thereof. 
 IN WITNESS WHEREOF, the undersigned has executed this Joinder Agreement as of the 30th day of October, 2013. 
  

					
	 NOVO A/S

		
	By 	 	/s/ Jack B. Nielsen
		 	Name: Jack B. Nielsen
		 	Title:	 	Partner
		 		 	 Novo Ventures

		 		 	 Tuborg Havnevej 19

		 		 	 DK-2900 Hellerup