Document:

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 HellerupPrepared by R.R. Donnelley Financial -- EX-10.22

 Exhibit 10.22 

CYMABAY THERAPEUTICS, INC. 

INCENTIVE AWARD GRANT NOTICE 

(2013 EQUITY PLAN) 

CymaBay Therapeutics, Inc. (the “Company”), pursuant to its 2013 Equity Plan (the “Plan”), hereby grants to
Holder an incentive award (the “Award”) which shall be settled, at the sole discretion of the Company, by either (1) Holder’s purchase of the number of shares of the Company’s Common Stock at the Exercise Price
(Per Share) as set forth below or (2) Holder’s receipt of a cash payment equal to the excess of the Fair Market Value of one share of the Company’s common stock on the date of exercise over the Exercise Price (Per Share) multiplied by
the portion of the Award being exercised, not to exceed the Number of Shares Subject to Award as set for the below. This Award is subject to all of the terms and conditions as set forth in this notice, in the Incentive Award Agreement, the Plan and
the Notice of Exercise, all of which are attached hereto and incorporated herein in their entirety. Capitalized terms not explicitly defined herein but defined in the Plan or the Incentive Award Agreement will have the same definitions as in the
Plan or the Incentive Award Agreement. If there is any conflict between the terms in this notice and the Plan, the terms of the Plan will control. 
  

			
	 Holder:
	 	  

	 Date of Grant:
	 	  

	 Vesting Commencement Date:
	 	  

	 Number of Shares Subject to Award:
	 	  

	 Exercise Price (Per Share):
	 	  

	 Total Exercise Price:
	 	  

	 Expiration Date:
	 	  

  

	Type of Grant:	x Incentive Award 

  

	Exercise Schedule:	x Same as Vesting Schedule 

  

	Vesting Schedule:	This Award shall vest as set forth in provision (A) below, provided however, in the event the matters contemplated by provision (A) do not occur, then this Award shall vest as set forth in provision
(B) below: 

 (A) in the event the Company’s stockholders approve an increase to authorized number
of shares reserved under the Plan before the second anniversary of the Date of Grant, then 1/48 of the shares subject to the Award shall vest and be exercisable (retroactive to the Date of Grant) each month as measured from the Date of Grant,
subject to Holder’s Continuous Service as of such date; provided, however, 100% of the shares subject to the Award shall accelerate and be fully exercisable immediately prior to the consummation of any Change of Control. 

(B) In the event the Company’s stockholders do not approve an increase to the authorized number of shares reserved
under the Plan before the second anniversary of the Date of Grant, then 100% of the shares subject to the Award shall vest in full and be fully exercisable on the second anniversary of the Date of Grant, subject to Holder’s Continuous Service
as of such date; provided, however, 100% of the shares subject to the Award shall accelerate and be fully exercisable immediately prior to the consummation of any Change of Control. 

 

	Payment:	If the Company elects to settle the Award in shares of Common Stock, then by one or a combination of the following items (described in the Incentive Award Agreement): 

 

	    	x By cash, check, bank draft or money order payable to the Company 

  

	    	x Pursuant to a Regulation T Program if the shares are publicly traded 

  
 1. 

 Additional Terms/Acknowledgements: Holder acknowledges receipt of, and understands and agrees to, this
Incentive Award Grant Notice, the Incentive Award Agreement and the Plan. Holder acknowledges and agrees that this Incentive Award Grant Notice and the Incentive Award Agreement may not be modified, amended or revised except as provided in the Plan.
Holder further acknowledges that as of the Date of Grant, this Incentive Award Grant Notice, the Incentive Award Agreement, and the Plan set forth the entire understanding between Holder and the Company regarding this Award and supersede all prior
oral and written agreements, promises and/or representations on that subject with the exception of (i) options or awards previously granted and delivered to Holder, (ii) any compensation recovery policy that is adopted by the Company or is
otherwise required by applicable law and (iii) any written employment or severance arrangement that would provide for vesting acceleration of this Award upon the terms and conditions set forth therein. 

By accepting this Award, Holder consents to receive such documents by electronic delivery and to participate in the Plan through an online or electronic
system established and maintained by the Company or another third party designated by the Company. 
  

									
	CYMABAY THERAPEUTICS, INC.	 		 	HOLDER:
				
	By:	 	 	 		 	 
		 	Signature	 		 	Signature
					
	 Title:
	 	 	 		 	Date:	 	 
				
	 Date:
	 	 	 		 	

 ATTACHMENTS: Incentive Award Agreement, 2013 Equity Plan and Notice of Exercise 

  
 2. 

 ATTACHMENT I 

INCENTIVE AWARD AGREEMENT 

 CYMABAY THERAPEUTICS, INC. 

2013 EQUITY PLAN 

INCENTIVE AWARD AGREEMENT 

Pursuant to your Incentive Award Grant Notice (“Grant Notice”) and this Incentive Award Agreement, CymaBay
Therapeutics, Inc. (the “Company”) has granted you an Award under its 2013 Equity Plan (the “Plan”) which shall be settled, at the sole discretion of the Company, by either (1) Holder’s
purchase of the number of shares of the Company’s Common Stock at the Exercise Price (Per Share) set forth on the Grant Notice or (2) Holder’s receipt in a cash payment equal to the excess of the Fair Market Value of one share of the
Company’s common stock on the date of exercise over the Exercise Price (Per Share) as set forth on the Grant Notice multiplied by the portion of the Award being exercised, not to exceed the Number of Shares Subject to Award as set forth on the
Grant Notice. The Award is granted to you effective as of the date of grant set forth in the Grant Notice (the “Date of Grant”). If there is any conflict between the terms in this Incentive Award Agreement and the Plan, the
terms of the Plan will control. Capitalized terms not explicitly defined in this Incentive Award Agreement or in the Grant Notice but defined in the Plan will have the same definitions as in the Plan. 

The details of your Award, in addition to those set forth in the Grant Notice and the Plan, are as follows: 

1. VESTING. Subject to the provisions contained herein, your Award will vest as provided in your Grant Notice. Vesting
will cease upon the termination of your Continuous Service. 
 2. NUMBER OF SHARES
AND EXERCISE PRICE. The number of shares of Common Stock subject to your Award and your exercise price per share in your Grant Notice will be adjusted for Capitalization Adjustments. 

3. EXERCISE RESTRICTION FOR NON-EXEMPT
EMPLOYEES. If you are an Employee eligible for overtime compensation under the Fair Labor Standards Act of 1938, as amended (that is, a “Non-Exempt Employee”), and except as otherwise provided
in the Plan, you may not exercise your Award until you have completed at least six (6) months of Continuous Service measured from the Date of Grant, even if you have already been an employee for more than six (6) months. Consistent with
the provisions of the Worker Economic Opportunity Act, you may exercise your Award as to any vested portion prior to such six (6) month anniversary in the case of (i) your death or disability, (ii) a Corporate Transaction in which
your Award is not assumed, continued or substituted, (iii) a Change in Control or (iv) your termination of Continuous Service on your “retirement” (as defined in the Company’s benefit plans).  

  
 1. 

 4. METHOD OF
PAYMENT. If the Company elects to settle the Award in shares of Common Stock, then you must pay the full amount of the exercise price for the shares you wish to exercise. In such case, you may pay the exercise price
in cash or by check, bank draft or money order payable to the Company or in any other manner permitted by your Grant Notice, which may include one or more of the following: 

(a) Provided that at the time of exercise the Common Stock is publicly traded, pursuant to a program developed under Regulation T as
promulgated by the Federal Reserve Board that, prior to the issuance of Common Stock, results in either the receipt of cash (or check) by the Company or the receipt of irrevocable instructions to pay the aggregate exercise price to the Company from
the sales proceeds. This manner of payment is also known as a “broker-assisted exercise”, “same day sale”, or “sell to cover”. 

(b) Provided that at the time of exercise the Common Stock is publicly traded, by delivery to the Company (either by actual delivery or
attestation) of already-owned shares of Common Stock that are owned free and clear of any liens, claims, encumbrances or security interests, and that are valued at Fair Market Value on the date of exercise. “Delivery” for these purposes,
in the sole discretion of the Company at the time you exercise your Award, will include delivery to the Company of your attestation of ownership of such shares of Common Stock in a form approved by the Company. You may not exercise your Award by
delivery to the Company of Common Stock if doing so would violate the provisions of any law, regulation or agreement restricting the redemption of the Company’s stock. 

(c) Subject to the consent of the Company at the time of exercise, by a “net exercise” arrangement pursuant to which the
Company will reduce the number of shares of Common Stock issued upon exercise of your Award by the largest whole number of shares with a Fair Market Value that does not exceed the aggregate exercise price. You must pay any remaining balance of the
aggregate exercise price not satisfied by the “net exercise” in cash or other permitted form of payment. Shares of Common Stock will no longer be outstanding under your Award and will not be exercisable thereafter if those shares
(i) are used to pay the exercise price pursuant to the “net exercise,” (ii) are delivered to you as a result of such exercise, and (iii) are withheld to satisfy your tax withholding obligations. 

5. WHOLE SHARES. You may exercise your Award only for whole shares of Common Stock. 

6. SECURITIES LAW COMPLIANCE. In no event may you exercise your Award unless the shares of
Common Stock issuable upon exercise are then registered under the Securities Act or, if not registered, the Company has determined that your exercise and the issuance of the shares would be exempt from the registration requirements of the Securities
Act. The exercise of your Award also must comply with all other applicable laws and regulations governing your Award, and you may not exercise your Award if the Company determines that such exercise would not be in material compliance with such laws
and regulations (including any restrictions on exercise required for compliance with Treas. Reg. 1.401(k)-1(d)(3), if applicable). 

7. TERM. You may not exercise your Award before the Date of Grant or after the expiration of the Award’s term. The
term of your Award expires, subject to the provisions of Section 5(h) of the Plan, upon the earliest of the following: 
 (a)
immediately upon the termination of your Continuous Service for Cause; 

  
 2. 

 (b) three (3) months after the termination of your Continuous Service for any reason
other than Cause, your Disability or your death (except as otherwise provided in Section 7(d) below); provided, however, that if during any part of such three (3) month period your Award is not exercisable solely because of the
condition set forth in the section above relating to “Securities Law Compliance,” your Award will not expire until the earlier of the Expiration Date or until it has been exercisable for an aggregate period of three (3) months after
the termination of your Continuous Service; provided further, if during any part of such three (3) month period, the sale of any Common Stock received upon exercise of your Award would violate the Company’s insider trading policy,
then your Award will not expire until the earlier of the Expiration Date or until it has been exercisable for an aggregate period of three (3) months after the termination of your Continuous Service during which the sale of the Common Stock
received upon exercise of your Award would not be in violation of the Company’s insider trading policy. Notwithstanding the foregoing, if (i) you are a Non-Exempt Employee, (ii) your Continuous Service terminates within six
(6) months after the Date of Grant, and (iii) you have vested in a portion of your Award at the time of your termination of Continuous Service, your Award will not expire until the earlier of (x) the later of (A) the date that is
seven (7) months after the Date of Grant, and (B) the date that is three (3) months after the termination of your Continuous Service, and (y) the Expiration Date; 

(c) twelve (12) months after the termination of your Continuous Service due to your Disability (except as otherwise provided in
Section 8(d)) below; 
 (d) eighteen (18) months after your death if you die either during your Continuous Service or
within three (3) months after your Continuous Service terminates for any reason other than Cause; 
 (e) the Expiration Date
indicated in your Grant Notice; or 
 (f) the day before the tenth (10th) anniversary of the Date of Grant. 

8. EXERCISE. 

(a) You may exercise the vested portion of your Award during its term by (i) delivering a Notice of Exercise (in a form designated
by the Company) or completing such other documents and/or procedures designated by the Company for exercise and (ii) at the sole discretion of the Company, either paying the exercise price and any applicable withholding taxes to the
Company’s Secretary, stock plan administrator, or such other person as the Company may designate, together with such additional documents as the Company may then require or acceptance of the cash value of the Award as determined on your Grant
Notice less any applicable withholding taxes. 
 (b) By exercising your Award you agree that, as a condition to any exercise of your
Award, the Company may require you to enter into an arrangement providing for the payment by you to the Company of any tax withholding obligation of the Company arising by reason of (i) the exercise of your Award, (ii) the lapse of any
substantial risk of forfeiture to which the shares of Common Stock are subject at the time of exercise, or (iii) the disposition of shares of Common Stock acquired upon such exercise. 

  
 3. 

 9. TRANSFERABILITY. Except as otherwise provided in this Section 9,
your Award is not transferable, except by will or by the laws of descent and distribution, and is exercisable during your life only by you. 

(a) Certain Trusts. Upon receiving written permission from the Board or its duly authorized designee, you may transfer your Award to a
trust if you are considered to be the sole beneficial owner (determined under Section 671 of the Code and applicable state law) while the Award is held in the trust. You and the trustee must enter into transfer and other agreements required by
the Company. 
 (b) Domestic Relations Orders. Upon receiving written permission from the Board or its duly authorized designee, and
provided that you and the designated transferee enter into transfer and other agreements required by the Company, you may transfer your Award pursuant to the terms of a domestic relations order, official marital settlement agreement or other divorce
or separation instrument as permitted by Treasury Regulation 1.421-1(b)(2) that contains the information required by the Company to effectuate the transfer. You are encouraged to discuss the proposed terms of any division of this Award with the
Company prior to finalizing the domestic relations order or marital settlement agreement to help ensure the required information is contained within the domestic relations order or marital settlement agreement. 

(c) Beneficiary Designation. Upon receiving written permission from the Board or its duly authorized designee, you may, by delivering
written notice to the Company, in a form approved by the Company and any broker designated by the Company to handle Award exercises, designate a third party who, on your death, will thereafter be entitled to exercise this Award and receive the
Common Stock or other consideration resulting from such exercise. In the absence of such a designation, your executor or administrator of your estate will be entitled to exercise this Award and receive, on behalf of your estate, the Common Stock or
other consideration resulting from such exercise. 
 10. AWARD NOT A SERVICE
CONTRACT. Your Award is not an employment or service contract, and nothing in your Award will be deemed to create in any way whatsoever any obligation on your part to continue in the employ of the Company or an
Affiliate, or of the Company or an Affiliate to continue your employment. In addition, nothing in your Award will obligate the Company or an Affiliate, their respective stockholders, boards of directors, officers or employees to continue any
relationship that you might have as a Director or Consultant for the Company or an Affiliate. 
 11. WITHHOLDING
OBLIGATIONS. 
 (a) At the time you exercise your Award, in whole or in part, and at any time
thereafter as requested by the Company, you hereby authorize withholding from payroll and any other amounts payable to you, and otherwise agree to make adequate provision for (including by means of a “same day sale” pursuant to a program
developed under Regulation T as promulgated by the Federal Reserve Board to the extent permitted by the Company), any sums required to satisfy the federal, state, local and foreign tax withholding obligations of the Company or an Affiliate, if any,
which arise in connection with the exercise of your Award. 

  
 4. 

 (b) Upon your request and subject to approval by the Company, and compliance with any
applicable legal conditions or restrictions, the Company may withhold from fully vested shares of Common Stock otherwise issuable to you upon the exercise of your Award a number of whole shares of Common Stock having a Fair Market Value, determined
by the Company as of the date of exercise, not in excess of the minimum amount of tax required to be withheld by law (or such lower amount as may be necessary to avoid classification of your Award as a liability for financial accounting purposes).
If the date of determination of any tax withholding obligation is deferred to a date later than the date of exercise of your Award, share withholding pursuant to the preceding sentence shall not be permitted unless you make a proper and timely
election under Section 83(b) of the Code, covering the aggregate number of shares of Common Stock acquired upon such exercise with respect to which such determination is otherwise deferred, to accelerate the determination of such tax
withholding obligation to the date of exercise of your Award. Notwithstanding the filing of such election, shares of Common Stock shall be withheld solely from fully vested shares of Common Stock determined as of the date of exercise of your Award
that are otherwise issuable to you upon such exercise. Any adverse consequences to you arising in connection with such share withholding procedure shall be your sole responsibility. 

(c) You may not exercise your Award unless the tax withholding obligations of the Company and/or any Affiliate are satisfied.
Accordingly, you may not be able to exercise your Award when desired even though your Award is vested, and the Company will have no obligation to issue a certificate for such shares of Common Stock or release such shares of Common Stock from any
escrow provided for herein, if applicable, unless such obligations are satisfied. 
 12. TAX
CONSEQUENCES. You hereby agree that the Company does not have a duty to design or administer the Plan or its other compensation programs in a manner that minimizes your tax liabilities. You will not make any claim
against the Company, or any of its Officers, Directors, Employees or Affiliates related to tax liabilities arising from your Award or your other compensation. In particular, you acknowledge that this Award is exempt from Section 409A of the
Code only if the exercise price per share specified in the Grant Notice is at least equal to the “fair market value” per share of the Common Stock on the Date of Grant and there is no other impermissible deferral of compensation associated
with the Award. 
 13. NOTICES. Any notices provided for in your Award or the Plan will be given in
writing (including electronically) and will be deemed effectively given upon receipt or, in the case of notices delivered by mail by the Company to you, five (5) days after deposit in the United States mail, postage prepaid, addressed to you at
the last address you provided to the Company. The Company may, in its sole discretion, decide to deliver any documents related to participation in the Plan and this Award by electronic means or to request your consent to participate in the Plan by
electronic means. By accepting this Award, you consent to receive such documents by electronic delivery and to participate in the Plan through an on-line or electronic system established and maintained by the Company or another third party
designated by the Company. 

  
 5. 

 14. GOVERNING PLAN DOCUMENT.
Your Award is subject to all the provisions of the Plan, the provisions of which are hereby made a part of your Award, and is further subject to all interpretations, amendments, rules and regulations, which may from time to time be promulgated and
adopted pursuant to the Plan. If there is any conflict between the provisions of your Award and those of the Plan, the provisions of the Plan will control. In addition, your Award (and any compensation paid or shares issued under your Award) is
subject to recoupment in accordance with The Dodd–Frank Wall Street Reform and Consumer Protection Act and any implementing regulations thereunder, any clawback policy adopted by the Company and any compensation recovery policy otherwise
required by applicable law. 
 15. OTHER DOCUMENTS. You hereby acknowledge receipt of
and the right to receive a document providing the information required by Rule 428(b)(1) promulgated under the Securities Act, which includes the Plan prospectus. In addition, you acknowledge receipt of the Company’s policy permitting certain
individuals to sell shares only during certain “window” periods and the Company’s insider trading policy, in effect from time to time. 

16. EFFECT ON OTHER EMPLOYEE BENEFIT
PLANS. The value of this Award will not be included as compensation, earnings, salaries, or other similar terms used when calculating your benefits under any employee benefit plan sponsored by the Company or any
Affiliate, except as such plan otherwise expressly provides. The Company expressly reserves its rights to amend, modify, or terminate any of the Company’s or any Affiliate’s employee benefit plans. 

17. VOTING RIGHTS. You will not have voting or any other rights as a stockholder of the
Company with respect to the shares to be issued pursuant to this Award until such shares are issued to you. Upon such issuance, you will obtain full voting and other rights as a stockholder of the Company. Nothing contained in this Award, and no
action taken pursuant to its provisions, will create or be construed to create a trust of any kind or a fiduciary relationship between you and the Company or any other person. 

18. SEVERABILITY. If all or any part of this Incentive Award Agreement or the Plan is declared by any
court or governmental authority to be unlawful or invalid, such unlawfulness or invalidity will not invalidate any portion of this Incentive Award Agreement or the Plan not declared to be unlawful or invalid. Any Section of this Incentive Award
Agreement (or part of such a Section) so declared to be unlawful or invalid shall, if possible, be construed in a manner which will give effect to the terms of such Section or part of a Section to the fullest extent possible while remaining lawful
and valid. 
 19. MISCELLANEOUS. 

(a) The rights and obligations of the Company under your Award will be transferable to any one or more persons or entities, and all
covenants and agreements hereunder will inure to the benefit of, and be enforceable by the Company’s successors and assigns. 

(b) You agree upon request to execute any further documents or instruments necessary or desirable in the sole determination of the
Company to carry out the purposes or intent of your Award. 
 (c) You acknowledge and agree that you have reviewed your Award in its
entirety, have had an opportunity to obtain the advice of counsel prior to executing and accepting your Award, and fully understand all provisions of your Award. 

  
 6. 

 (d) This Incentive Award Agreement will be subject to all applicable laws, rules, and
regulations, and to such approvals by any governmental agencies or national securities exchanges as may be required. 
 (e) All
obligations of the Company under the Plan and this Incentive Award Agreement will be binding on any successor to the Company, whether the existence of such successor is the result of a direct or indirect purchase, merger, consolidation, or
otherwise, of all or substantially all of the business and/or assets of the Company. 
 *    *    *

 This Incentive Award Agreement will be deemed to be signed by you upon the 

signing by you of the Grant Notice to which it is attached. 

  
 7. 

 ATTACHMENT II 

2013 EQUITY PLAN 

 ATTACHMENT III 

NOTICE OF EXERCISE 

 NOTICE OF EXERCISE 

CymaBay Therapeutics, Inc. 
 Attention: [Stock Plan
Administrator] 
 3876 Bay Center Place 
 Hayward, CA 94545 

Date of Exercise:
                                 

This constitutes notice to CymaBay Therapeutics, Inc. (the “Company”) under my Award that I elect to exercise my Award
with respect to the number of shares of Common Stock of the Company (the “Shares”) set forth below. If the Company elects to settle the Award in shares of Common Stock, then I agree to pay the exercise price set forth
below. 
 If Award is settled in Cash: 
  

							
	 Award dated:
	 		  	  
	  	
				
	 Number of Shares as to which Award is exercised:
	 		  	  
	  	
				
	 Fair Market Value of one Share as of Date of Exercise
	 		  	  
	  	
				
	 Exercise Price of one Share pursuant to Award Grant Notice
	 		  	  
	  	
				
	 The aggregate Cash value as of the Date of Exercise
	 		  	  
	  	
				
	 If Award is settled in Stock:
	 		  		  	
				
	 Award dated:
	 		  		  	
				
	 Number of Shares as to which Award is exercised:
	 		  	  
	  	
				
	 Exercise Price of one Share pursuant to Award Grant Notice
	 		  	  
	  	
				
	 Certificates to be issued in name of:
	 		  	  
	  	
				
	 Total exercise price:
	 	 $
	  	  
	  	
				
	 Cash payment delivered herewith:
	 		  	$                            	  	
				
	 Regulation T Program (cashless exercise):
	 		  	$                            	  	

 By this exercise, I agree (i) to provide such additional documents as you may require pursuant to the
terms of the CymaBay Therapeutics, Inc. 2013 Equity Plan, and (ii) in the event the Company elects for the Award to be settled in Shares, to provide for the payment by me to you (in the manner designated by you) of your withholding obligation,
if any, relating to the exercise of this Award. 

 I hereby make the following certifications and representations with respect to the number of
Shares listed above, which are being acquired by me for my own account upon exercise of the Award as set forth above: 
 I acknowledge that
the Shares have not been registered under the Securities Act of 1933, as amended (the “Securities Act”), and are deemed to constitute “restricted securities” under Rule 701 and Rule 144 promulgated under the
Securities Act. I warrant and represent to the Company that I have no present intention of distributing or selling said Shares, except as permitted under the Securities Act and any applicable state securities laws. 

I further acknowledge that I will not be able to resell the Shares for at least ninety (90) days after the stock of the Company becomes
publicly traded (i.e., subject to the reporting requirements of Section 13 or 15(d) of the Securities Exchange Act of 1934) under Rule 701 and that more restrictive conditions apply to affiliates of the Company under Rule 144. 

I further acknowledge that all certificates representing any of the Shares subject to the provisions of the Award shall have endorsed thereon
appropriate legends reflecting the foregoing limitations, as well as any legends reflecting restrictions pursuant to the Company’s Articles of Incorporation, Bylaws and/or applicable securities laws. 

I further agree that, if required by the Company (or a representative of the underwriters) in connection with the first underwritten
registration of the offering of any securities of the Company under the Securities Act, I will not sell, dispose of, transfer, make any short sale of, grant any option for the purchase of, or enter into any hedging or similar transaction with the
same economic effect as a sale with respect to any shares of Common Stock or other securities of the Company for a period of one hundred eighty (180) days following the effective date of a registration statement of the Company filed under the
Securities Act (or such longer period as the underwriters or the Company shall request to facilitate compliance with FINRA Rule 2711 or NYSE Member Rule 472 or any successor or similar rule or regulation) (the “Lock-Up
Period”). I further agree to execute and deliver such other agreements as may be reasonably requested by the Company or the underwriters that are consistent with the foregoing or that are necessary to give further effect thereto. In
order to enforce the foregoing covenant, the Company may impose stop-transfer instructions with respect to securities subject to the foregoing restrictions until the end of such period. 

 

	
	Very truly yours,
	
	   

	

  
 2.

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