Document:

Fifth Agreement Regarding Private Placement of Securities

 EXHIBIT 10.1 

FIFTH AGREEMENT REGARDING PRIVATE PLACEMENT OF SECURITIES 
 OF 
 SUNESIS PHARMACEUTICALS, INC. 

THIS AGREEMENT (the “Agreement”) is made and entered
into as of this 2nd day of February, 2012, by and among
SUNESIS PHARMACEUTICALS, INC., a Delaware corporation (the “Company”), and the persons and entities listed on Exhibit A hereto (the
“Investors”). 
 RECITALS 

A. The Company and the Investors wish to amend that certain Investor Rights Agreement, dated April 3, 2009, as amended
June 29, 2009, October 27, 2009 and March 29, 2010 (as amended, the “Rights Agreement”), by and among the Company and the Investors (as defined in the Rights Agreement); 

B. Pursuant to Section 8(c) of the Rights Agreement, Section 7(b) of the Rights Agreement may be amended, modified,
supplemented or waived only by written consent of the Company, the Majority Investors (as defined in the Rights Agreement) and Alta Partners, Bay City Capital, NEA and Nextech (each as defined in the Rights Agreement); and 

C. The undersigned hold a majority-in-interest of the total Registrable Securities outstanding and constitute the Majority
Investors and include Alta Partners, Bay City Capital, NEA and Nextech (collectively, the “Requisite Investors”). 
 AGREEMENT 
 NOW,
THEREFORE, in consideration of these premises and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as follows: 

1. AMENDMENT TO RIGHTS AGREEMENT. All capitalized terms not
otherwise defined in this Section 2 shall be as defined in the Rights Agreement. The Company and the undersigned agree that Section 7(b)(2) of the Rights Agreement be, and it hereby is, amended and restated to read as follows: 

“Subject to Section 7(b)(6) below, from and after the earlier to occur of (i) the Second Unit Closing,
(ii) the Common Equity Closing and (iii) the closing of an Alternative Common Stock Financing in which the Investors exercise preemptive rights pursuant to the terms of this Agreement and, as a result, beneficially own greater than a
majority of the Company’s voting stock as of such closing, the Company shall take all appropriate action to promptly establish and maintain the size of the Board at ten (10) members, five (5) of which shall be Investor
Designees and nominated in accordance with the provisions of this Section 7(b). Alta Partners, Bay City Capital, NEA and Nextech, together with their respective affiliates, shall each have the right to designate one (1) such Investor
Designee. Notwithstanding the foregoing, the Company’s obligation to set and maintain the size of the Board at ten (10) members and the Investors’ right to designate five (5) Investor Designees pursuant to this
Section 7(b)(2) shall not be effective prior to May 1, 2010 or such later date as determined by the Majority Investors. On or prior to January 20 of each year in which the Majority Investors have rights pursuant to this
Section 7(b) (assuming the Company has made a request therefor at least five (5) Trading Days prior thereto), and within five (5) Trading Days of the request by the Company in connection with the preparation of a proxy

  
 1. 

 
statement with respect to the election of members of the Board or a vacancy created on the Board by the resignation, death or disability of an Investor Designee or the failure of an Investor
Designee to be elected at a meeting of the Company at any time at which the Majority Investors have rights pursuant to this Section 7(b), each Investor shall notify the Company of the number of voting shares of the Company’s capital stock
beneficially owned by such Investor as of a date within five (5) Trading Days of the delivery of such notice.” 
 2.
MISCELLANEOUS. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original, but all of which together shall constitute one and the same instrument. A facsimile, telecopy
or other reproduction of this Agreement may be executed by one or more parties hereto and delivered by such party by facsimile or any similar electronic transmission device pursuant to which the signature of or on behalf of such party can be seen.
Such execution and delivery shall be considered valid, binding and effective for all purposes. At the request of any party hereto, all parties hereto agree to execute and deliver an original of this Agreement as well as any facsimile, telecopy or
other reproduction hereof. Other than as set forth herein, the Rights Agreement shall remain in full force and effect. All questions concerning the construction, validity, enforcement and interpretation of this Agreement shall be governed by and
construed and enforced in accordance with the internal laws of the State of California, without regard to the principles of conflicts of law thereof. Upon the execution of this Agreement by the Company and the Requisite Investors, all parties
to the Rights Agreement shall be bound by this Agreement. 
 [SIGNATURE PAGE TO
FOLLOW] 

  
 2. 

 IN WITNESS WHEREOF, the
parties hereto have executed this Agreement as of the date first above written. 
  

									
	COMPANY:	 		 	INVESTORS:
			
	SUNESIS PHARMACEUTICALS, INC.	 		 	BAY CITY CAPITAL FUND V, L.P.
					
	Signature:	 	/s/ Daniel N. Swisher, Jr.	 		 	By:	 	/s/ Carl Goldfischer
	Print Name:	 	Daniel N. Swisher, Jr.	 		 	Name:	 	Carl Goldfischer
	Title:	 	President and CEO	 		 	Title:	 	Managing Director
	Address:	 	 395 Oyster Point Boulevard, #400

South San Francisco, CA 94080
	 		 		 	
			
		 		 	BAY CITY CAPITAL FUND V CO-INVESTMENT FUND,
L.P.
					
		 		 		 	By:	 	/s/ Carl Goldfischer
		 		 		 	Name:	 	Carl Goldfischer
		 		 		 	Title:	 	Managing Director
		 		 		 		 	

 IN WITNESS WHEREOF, the
party hereto has executed this Agreement as of the date first above written. 
  

			
	GROWTH EQUITY OPPORTUNITIES FUND, LLC
		
	By:	 	/s/ Louis S. Citron
	Name:	 	Louis S. Citron
	Title:	 	Chief Legal Officer

 IN WITNESS WHEREOF, the
parties hereto have executed this Agreement as of the date first above written. 
  

			
	ALTA BIOPHARMA PARTNERS III, L.P.
	
	By: Alta BioPharma Management III, LLC
		
	By:	 	/s/ Hilary Strain
	Name:	 	Hilary Strain
	Title:	 	CFO
	
	ALTA BIOPHARMA PARTNERS III GMBH & CO. BETEILIGUNGS
KG
	
	By: Alta BioPharma Management III, LLC
		
	By:	 	/s/ Hilary Strain
	Name:	 	Hilary Strain
	Title:	 	CFO
	
	ALTA EMBARCADERO BIOPHARMA PARTNERS III, LLC
		
	By:	 	/s/ Hilary Strain
	Name:	 	Hilary Strain
	Title:	 	CFO

 Sunesis Pharmaceuticals, Inc. 

Fifth Agreement Regarding Private Placement of Securities – Signature Page 

 IN WITNESS WHEREOF, the
party hereto has executed this Agreement as of the date first above written. 
  

			
	ONC GENERAL PARTNER LIMITED AS GENERAL PARTNER OF ONC
PARTNERS, L.P.
		
	By:	 	/s/ Michael Robinson
	Name:	 	Michael Robinson
	Title:	 	Director

 Sunesis Pharmaceuticals, Inc. 

Fifth Agreement Regarding Private Placement of Securities – Signature Page 

 IN WITNESS WHEREOF, the
party hereto has executed this Agreement as of the date first above written. 
  

			
	SWISHER REVOCABLE TRUST
		
	By:	 	/s/ Daniel N. Swisher, Jr.
	Name:	 	Daniel N. Swisher, Jr.
	Title:	 	Trustee

 Sunesis Pharmaceuticals, Inc. 

Fifth Agreement Regarding Private Placement of Securities – Signature Page 

 IN WITNESS WHEREOF, the
party hereto has executed this Agreement as of the date first above written. 
  

			
	BJERKHOLT/HAHN FAMILY TRUST
		
	By:	 	/s/ Eric Bjerkholt
	Name:	 	Eric Bjerkholt
	Title:	 	Trustee

 Sunesis Pharmaceuticals, Inc. 

Fifth Agreement Regarding Private Placement of Securities – Signature Page 

 IN WITNESS WHEREOF, the
party hereto has executed this Agreement as of the date first above written. 
  

			
	STEVEN BLAKE KETCHUM
		
	By:	 	/s/ Steven Blake Ketchum

 Sunesis Pharmaceuticals, Inc. 

Fifth Agreement Regarding Private Placement of Securities – Signature Page 

 EXHIBIT A 

LIST OF INVESTORS 
 Bay City Capital Fund V, L.P. 
 Bay City Capital Fund V Co-Investment Fund, L.P. 

Growth Equity Opportunities Fund, LLC 
 Alta
BioPharma Partners III, L.P. 
 Alta BioPharma Partners III GmbH & Co. Beteiligungs KG 

Alta Embarcadero BioPharma Partners III, LLC 

Merlin Nexus III, L.P. 
 Nexus Gemini, L.P.

 ONC General Partner Limited as General Partner of ONC Partners, L.P. 
 Vision Opportunity Master Fund, Ltd. 
 Caxton Advantage Life Sciences Fund, L.P. 

Venrock Associates 
 Venrock Associates II,
L.P. 
 Opus Point Healthcare (Low Net) Fund, L.P. 
 Opus Point Healthcare Value Fund, L.P. 
 Swisher Revocable Trust 

Bjerkholt/Hahn Family Trust 
 Steven Blake
KetchumLetter Agreement

 EXHIBIT 10.2 
 February 2, 2012 
 Steven B. Ketchum 
 49 Canoe Brook Lane 
 Far Hills, NJ 07931-2808 

 

	Re:	Change of Status 

 Dear Steve: 

This letter confirms that you have tendered your resignation to the Company, effective February 15, 2012, and the Company hereby accepts that
resignation effective that day. You acknowledge and agree that you are not entitled to any severance benefits from the Company arising from your resignation of employment. 
 The Board of Directors has approved your appointment to the Board, effective as of February 15, 2012. In that role, you will be eligible for the standard Board retainer of $30,000 per year, payable
on the date of our annual stockholders’ meeting (typically held in June). You currently have four option grants, all of which shall continue to vest until June 30, 2012 (or earlier if your Board service ends prior to that date). You hereby
agree that all stock options held by you that do not vest on or before June 30, 2012 shall be forfeited by you. Your vested stock options will remain exercisable during your Board service in accordance with the terms of the applicable stock
option agreements. In your capacity as a Board member, you will remain eligible for periodic equity grants as determined by the Board in its sole discretion. 
 The Board has also approved a bonus payment to you in accordance with the Company’s 2011 Bonus Program in the amount of $95,700, less standard payroll deductions and withholdings. The bonus payment
shall be made concurrently with payments to other participants in the 2011 Bonus Program, which is expected to occur in the first quarter of 2012. 
 We appreciate your service to the Company, and look forward to working with you in your new role as a Director. 
  

	
	Best regards,
	
	/s/ Daniel N. Swisher, Jr.
	Daniel N. Swisher, Jr.
	President and Chief Executive Officer

  

					
	ACCEPTED AND AGREED TO:	 		 	
			
	/s/ Steven B. Ketchum	 		 	February 2, 2012
	Steven B. Ketchum	 		 	Date

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