Exhibit 10.1

FOURTH AGREEMENT REGARDING PRIVATE PLACEMENT OF SECURITIES

OF

SUNESIS PHARMACEUTICALS, INC.

THIS AGREEMENT (the “Agreement”) is made and entered into as of this 29th day of
March, 2010, 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 and October 27, 2009
(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 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 or have the right to acquire at least a
majority-in-interest of the total Unit Shares 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 hereby agree that Section 7(b)(2) of the Rights Agreement is hereby
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 nine (9) 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 nine
(9) 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 statement
with respect to the election of members of the Board or a vacancy created on

 

1.

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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.

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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/ Fred Craves

Print Name:  

Daniel N. Swisher, Jr.

     Name  

Fred Craves

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/ Fred Craves

       Name:  

Fred Craves

       Title:  

Managing Director

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GROWTH EQUITY OPPORTUNITIES FUND, LLC By:  

/s/ Charles W. Newton, III

Name:  

Charles W. Newton, III

Title:  

Manager of NEA 12 GP, LLC, which is

the general partner of NEA Partners 12, Limited Partnership, the general partner
of New Enterprise Associates 12, Limited Partnership, the sole shareholder of
Growth Equity Opportunities Fund, LLC

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ALTA BIOPHARMA PARTNERS III, L.P. By: Alta BioPharma Management III LLC By:  

/s/ Edward Hurwitz

Name:  

Edward Hurwitz

Title:  

Director

ALTA BIOPHARMA PARTNERS III GMBH & CO. BETEILIGUNGS KG By: Alta BioPharma
Management III LLC By:  

/s/ Edward Hurwitz

Name:  

Edward Hurwitz

Title:  

Director

ALTA EMBARCADERO BIOPHARMA PARTNERS III, LLC By:  

/s/ Edward Hurwitz

Name:  

Edward Hurwitz

Title:  

Manager

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ONC GENERAL PARTNER LIMITED AS GENERAL PARTNER OF ONC PARTNERS, L.P. By:  

/s/ Michael Robinson

Name:  

Michael Robinson

Title:  

Director

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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

ONC General Partner Limited as General Partner of ONC Partners, L.P.