UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549





FORM 10-Q/A

Amendment No. 1





(Mark One)

|x | QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ---------------------------------------------------------------------------------------

For the quarterly period ended March 31, 2011

OR



| ̈ | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934
|- | ----------------------------------------------------------------------------------------

For the transition period from              to

Commission file number: 000-51531





LOGO

SUNESIS PHARMACEUTICALS, INC.

(Exact Name of Registrant as Specified in its Charter)







|                                                               |  |                                        
|-------------------------------------------------------------- |  | ---------------------------------------
|Delaware                                                       |  | 94-3295878                             
|(State or Other Jurisdiction of
Incorporation or Organization) |  | (I.R.S. Employer Identification Number)

395 Oyster Point Boulevard,
Suite 400

South San Francisco, California 94080

(Address of Principal Executive Offices including Zip Code)

(650) 266-3500

(Registrants Telephone Number, Including Area Code)





Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the
Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file reports), and (2) has been subject to such filing requirements for the past 90
days.    Yes  x    No   ̈



Indicate by check mark whether
the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T during the preceding 12 months (or for such shorter
period that the registrant was required to submit and post such files).    Yes   ̈    No   ̈

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or
a smaller reporting company. See the definitions of large accelerated filer, accelerated filer and smaller reporting company in Rule 12b-2 of the Exchange Act. (Check one):



|                        |  |                                                  |  |                           |  |  
|----------------------- |  | ------------------------------------------------ |  | ------------------------- |  | -
|Large accelerated filer |  |  ̈                                                |  | Accelerated filer         |  |  ̈
|                        |  |                                                  | 
|Non-accelerated filer   |  |  ̈  (Do not check if a smaller reporting company) |  | Smaller reporting company |  | x

Indicate by check mark whether the registrant is a shell company (as defined in Exchange Act
Rule 12b-2).    Yes   ̈    No  x

The registrant had 46,027,474 shares of common stock, $0.0001 par value per share, outstanding as of April 30, 2011.









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SUNESIS PHARMACEUTICALS, INC.

QUARTERLY REPORT ON FORM 10-Q/A

FOR THE QUARTER ENDED MARCH 31, 2011

Explanatory Note to Form 10-Q
Amendment No. 1

This Amendment No. 1 (this Amendment) to the Quarterly Report on Form 10-Q for the
quarter ended March 31, 2011 (the Form 10-Q) of Sunesis Pharmaceuticals, Inc. is being filed for the purpose of re-filing Exhibits 10.4 and 10.5 to the Form 10-Q in response to comments received from the Securities and
Exchange Commission (the SEC) in connection with a pending request for confidential treatment of portions of such exhibits. In addition, as required by Rule 12b-15 under the Securities Exchange Act of 1934, as amended, new certifications
by the registrants principal executive officer and principal financial officer are filed as exhibits hereto.

No attempt
has been made in this Amendment to modify or update the other disclosures presented in the Form 10-Q. This Amendment does not reflect events occurring after the filing of the Form 10-Q (i.e., occurring after May 12, 2011) or modify or update
those disclosures that may be affected by subsequent events. Such subsequent matters are addressed in subsequent reports filed by the registrant with the SEC. Accordingly, this Amendment should be read in conjunction with the Form 10-Q and the
registrants other filings with the SEC.



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SIGNATURE

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized.



|                    |  |                                                                                                                            
|------------------- |  | ---------------------------------------------------------------------------------------------------------------------------
|                    |  | SUNESIS PHARMACEUTICALS, INC.                                                                                              
|                    |  | (Registrant)                                                                                                               
|                    | 
|Date: June 30, 2011 |  | /s/ Eric H. Bjerkholt                                                                                                      
|                    |  | Eric H. Bjerkholt Senior Vice President, Corporate Development and Finance, Chief Financial
Officer and Corporate Secretary



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EXHIBIT INDEX



|              |  |                                                                                                                                                     |  |                           |  |          |            |  |         |      |             |  |            |               |  |  |   | 
|------------- |  | --------------------------------------------------------------------------------------------------------------------------------------------------- |  | ------------------------- |  | -------- | ---------- |  | ------- | ---- | ----------- |  | ---------- | ------------- |  |  | - | 
|              |  |                                                                                                                                                     |  | Incorporated By Reference |  |          |            | 
|ExhibitNumber |  | Exhibit Description                                                                                                                                 |  | Form                      |  | File No. |            |  | Exhibit |      | Filing Date |  |            | FiledHerewith | 
|3.1           |  | Amended and Restated Certificate of Incorporation of the Registrant                                                                                 |  | 10-K/A                    |  |          | 000-51531  |  |         | 3.1  |             |  | 5/23/2007  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.2           |  | Amended and Restated Bylaws of the Registrant                                                                                                       |  | 8-K                       |  |          | 000-51531  |  |         | 3.2  |             |  | 12/11/2007 |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.3           |  | Certificate of Designation of the Series A Preferred Stock of the Registrant                                                                        |  | 8-K                       |  |          | 000-51531  |  |         | 3.3  |             |  | 4/3/2009   |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.4           |  | Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant                                                 |  | S-8                       |  |          | 333-160528 |  |         | 3.4  |             |  | 7/10/2009  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.5           |  | Certificate of Amendment to the Certificate of Designation of the Series A Preferred Stock of the Registrant                                        |  | 8-K                       |  |          | 000-51531  |  |         | 3.4  |             |  | 11/2/2009  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.6           |  | Certificate of Amendment to the Certificate of Designation of the Series A Preferred stock of the Registrant                                        |  | 8-K                       |  |          | 000-51531  |  |         | 3.5  |             |  | 1/21/2010  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|3.7           |  | Certificate of Amendment to the Amended and Restated Certificate of Incorporation of the Registrant                                                 |  | 8-K                       |  |          | 000-51531  |  |         | 3.1  |             |  | 2/14/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|4.1           |  | Reference is made to Exhibits 3.1, 3.2, 3.3, 3.4, 3.5, 3.6 and 3.7 above.                                                                           |  |                           |  |          |            |  |         |      |             |  |            |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|4.2           |  | Specimen Common Stock certificate of the Registrant                                                                                                 |  | 10-K                      |  |          | 000-51531  |  |         | 4.2  |             |  | 3/29/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|4.3           |  | Investor Rights Agreement, dated April 3, 2009, by and among the Registrant and the purchasers identified on the signature pages thereto            |  | 8-K                       |  |          | 000-51531  |  |         | 4.1  |             |  | 4/3/2009   |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.1*         |  | Sunesis Pharmaceuticals, Inc. 2011 Bonus Program                                                                                                    |  | 8-K                       |  |          | 000-51531  |  |         | 10.1 |             |  | 2/18/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.2          |  | Master Services Agreement, dated August 26, 2004, by and between the Registrant and Quintiles, Inc.                                                 |  | 10-Q                      |  |          | 000-51531  |  |         | 10.2 |             |  | 5/12/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.3          |  | First Amendment to Master Services Agreement, dated August 1, 2008, by and between the Registrant and Aptuit, Inc. (as assignee of Quintiles, Inc.) |  | 10-Q                      |  |          | 000-51531  |  |         | 10.3 |             |  | 5/12/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.4         |  | Amended and Restated Collaboration Agreement, dated March 31, 2011, by and between the Registrant and Biogen Idec MA Inc.                           |  |                           |  |          |            |  |         |      |             |  |            |               |  |  | X | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.5         |  | License Agreement, dated March 31, 2011, by and between the Registrant and Millennium Pharmaceuticals, Inc.                                         |  |                           |  |          |            |  |         |      |             |  |            |               |  |  | X | 
|              |  |                                                                                                                                                     |  |                           |  |         
|10.6         |  | Termination and Transition Agreement, dated March 31, 2011, by and between the Registrant, Biogen Idec MA Inc. and Millennium Pharmaceuticals, Inc. |  | 10-Q                      |  |          | 000-51531  |  |         | 10.6 |             |  | 5/12/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|31.1          |  | Certification of Chief Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act                                           |  | 10-Q                      |  |          | 000-51531  |  |         | 31.1 |             |  | 5/12/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|31.2          |  | Certification of Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act                                           |  | 10-Q                      |  |          | 000-51531  |  |         | 31.2 |             |  | 5/12/2011  |               |  |  |   | 
|              |  |                                                                                                                                                     |  |                           |  |         
|31.3          |  | Certification of Chief Executive Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act                                           |  |                           |  |          |            |  |         |      |             |  |            |               |  |  | X | 
|              |  |                                                                                                                                                     |  |                           |  |         
|31.4          |  | Certification of Chief Financial Officer pursuant to Rule 13a-14(a) or Rule 15d-14(a) of the Exchange Act                                           |  |                           |  |          |            |  |         |      |             |  |            |               |  |  | X | 
|              |  |                                                                                                                                                     |  |                           |  |         
|32.1#         |  | Certification of Chief Executive Officer and Chief Financial Officer pursuant to 13a-14(b) or 15d-14(b) of the Exchange Act                         |  | 10-Q                      |  |          | 000-51531  |  |         | 32.1 |             |  | 5/12/2011  |               |  |  |   | 



|* | Management contract, compensatory plan or arrangement.
|- | ------------------------------------------------------

| | Portions of the exhibit have been omitted pursuant to a request for confidential treatment. The omitted information has been filed separately with the Securities and
Exchange Commission.
|- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

|# | In accordance with Item 601(b)(32)(ii) of Regulation S-K and SEC Release Nos. 33-8238 and 34-47986, Final Rule; Managements Reports on Internal Control over
Financial Reporting and Certification of Disclosure in Exchange Act Periodic Reports, the Certification furnished in Exhibit 32.1 hereto is deemed to accompany this Form 10-K and will not be filed for purposes of Section 18 of the Exchange Act.
Such certification will not be deemed incorporated by reference into any filing under the Securities Act or the Exchange Act, except to the extent that the registrant specifically incorporates it by reference.
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