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As filed with the Securities and Exchange Commission on May 4, 2004

Registration No. 333-113488



SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549


Amendment No. 1
to
FORM S-3
REGISTRATION STATEMENT
Under
THE SECURITIES ACT OF 1933


DISCOVERY PARTNERS INTERNATIONAL, INC.
(Exact name of Registrant as specified in its charter)

Delaware
(State or other jurisdiction
of incorporation or organization)
  33-0655706
(I.R.S. Employer
Identification Number)

9640 Towne Centre Drive
San Diego, CA 92121
(858) 455-8600
(Address, including zip code, and telephone number, including area code, of Registrant's principal executive offices)


Craig Kussman
Chief Financial Officer
Discovery Partners International, Inc.
9640 Towne Centre Drive
San Diego, CA 92121
(858) 455-8600
(Name, address, including zip code, and telephone number, including area code, of agent for service)


Copies to:

L. Kay Chandler, Esq.
Matthew T. Browne, Esq.
Cooley Godward LLP
4401 Eastgate Mall
San Diego, CA 92121
Tel: (858) 550-6000
Fax: (858) 550-6420
  Jeffrey S. Marcus, Esq.
Tanisha M. Little, Esq.
Morrison & Foerster LLP
1290 Avenue of the Americas
New York, NY 10104-0012
Tel: (212) 468-8000
Fax: (212) 468-7900

Approximate date of commencement of proposed sale to the public:
As soon as practicable after this Registration Statement becomes effective.


        If the only securities being registered on this Form are being offered pursuant to dividend or interest reinvestment plans, please check the following box. o

        If any of the securities being registered on this Form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered in connection with dividend or interest reinvestment plans, check the following box. o

        If this Form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. o

        If this Form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering. o

        If delivery of the prospectus is expected to be made pursuant to Rule 434, please check the following box. o


CALCULATION OF REGISTRATION FEE


Title of Class of
Securities to be registered

  Amount to
Be registered(1)

  Proposed Maximum
Offering Price
Per Share(1)

  Proposed Maximum
Aggregate
Offering Price(1)

  Amount of
Registration fee(2)


Common Stock, $.001 par value per share, including related rights to purchase Series A Junior Participating Preferred Stock   8,305,300   $6.10   $50,662,330   $6,418.92

(1)
Of the 8,305,300 shares, 7,222,000 are being registered for resale by one of the registrant's stockholders and the remaining 1,083,300 shares are being registered for sale by the registrant in the event the underwriters exercise their over-allotment option in connection with the offering of the selling stockholder's shares. Estimated solely for the purpose of calculating the amount of the registration fee pursuant to Rule 457(c) of the Securities Act of 1933. The price per share and aggregate offering price are based upon the average of the high and low sales price of the registrant's common stock on March 3, 2004 as reported on the Nasdaq National Market.

(2)
Previously paid.


        The registrant hereby amends this registration statement on such date or dates as may be necessary to delay its effective date until the registrant shall file a further amendment which specifically states that this registration statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the registration statement shall become effective on such date as the Securities and Exchange Commission, acting pursuant to said Section 8(a), may determine.





EXPLANATORY NOTE

        Discovery Partners, Inc. has prepared this Amendment No. 1 to Registration Statement on Form S-3 (File No. 333-113488) for the purpose of filing with the Securities and Exchange Commission certain exhibits to the Registration Statement and amending Item 16 of the Registration Statement. This Amendment No. 1 to Registration Statement does not modify any other portion of the Registration Statement and accordingly no other portion of the Registration Statement has been included herein.



PART II

INFORMATION NOT REQUIRED IN PROSPECTUS

Item 16. Exhibits and Financial Statement Schedules

Exhibit
Number

  Description of Document
1.1   Form of Underwriting Agreement

4.1(1

)

Certificate of Incorporation of the Company (which was Exhibit No. 3.2 to the registrant's Form S-1 filed with the Securities and Exchange Commission on June 23, 2000 and is incorporated herein by this reference)

4.2(1

)

Bylaws of the Company (which was Exhibit 3.4 to the registrant's Form S-1 filed with the Securities and Exchange Committee on June 23, 2000 and is incorporated herein by this reference)

4.3(1

)

Rights Agreement, dated as of February 13, 2003, between Discovery Partners International, Inc. and American Stock Transfer & Trust Company, which includes the form of Certificate of Designation for the Series A junior participating preferred stock as Exhibit A, the form of Rights Certificate as Exhibit B and the Summary of Rights to Purchase Series A Preferred Stock as Exhibit C (which was Exhibit No. 4.2 to the registrant's Report on Form 8-K filed with the Securities and Exchange Committee on February 24, 2003 and is incorporated herein by this reference)

5.1

 

Opinion of Cooley Godward LLP

10.1(1

)

Second Amended and Restated Investors' Rights Agreement among us and the investors listed on Schedule A thereto, dated April 28, 2000, as amended. (which was Exhibit 10.2 to the registrant's Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on July 26, 2000 and is incorporated herein by this reference.)

10.2(1

)

Standstill Agreement between us and Axys Pharmaceuticals, Inc., dated April 28, 2000. (which was Exhibit 10.12 to the registrant's Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on May 9, 2000 and is incorporated herein by this reference.)

23.1(1

)

Consent of Ernst & Young LLP, Independent Auditors

24.1(1

)

Power of Attorney (included on signature page)

(1)
Previously filed.


SIGNATURES

        Pursuant to the requirements of the Securities Act of 1933, as amended, the registrant named below certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Amendment No. 1 to Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized, in the City of San Diego, State of California, on May 4, 2004.

      DISCOVERY PARTNERS INTERNATIONAL, INC.

 

 

By:

/s/  
RICCARDO PIGLIUCCI      
Riccardo Pigliucci
Chief Executive Officer and Chairman of the Board


POWER OF ATTORNEY

        Pursuant to the requirements of the Securities Act of 1933, as amended, this Amendment No. 1 to Registration Statement has been signed below by the following persons on behalf of Discovery Partners International, Inc. and in the capacities and on the dates indicated.

Date
  Signature
  Title

 

 

 

 

 
May 4, 2004   /s/  RICCARDO PIGLIUCCI      
Riccardo Pigliucci
  Chief Executive Officer and
Chairman of the Board

May 4, 2004

 

/s/  
CRAIG KUSSMAN      
Craig Kussman

 

Senior Vice President and
Chief Financial Officer
(Principal Financial and Accounting Officer)

May 4, 2004

 

/s/  
DIETER HOEHN*      
Dieter Hoehn

 

Director

May 4, 2004

 

/s/  
JOHN P. WALKER*      
John P. Walker

 

Director

May 4, 2004

 

/s/  
ALAN J. LEWIS*      
Alan J. Lewis

 

Director

May 4, 2004

 

/s/  
HARRY F. HIXSON, JR.*      
Harry F. Hixson, Jr.

 

Director

May 4, 2004

 

/s/  
COLIN T. DOLLERY*      
Colin T. Dollery

 

Director
         


May 4, 2004

 

/s/  
HERM ROSENMAN*      
Herm Rosenman

 

Director

May 4, 2004

 

/s/  
MICHAEL C. VENUTI*      
Michael C. Venuti

 

Director

*By:

 

/s/  
RICCARDO PIGLIUCCI      
Riccardo Pigliucci
Attorney-in-Fact

 

 

 

 


INDEX TO EXHIBITS

Exhibit
Number

  Description of Document
1.1   Form of Underwriting Agreement

4.1(1

)

Certificate of Incorporation of the Company (which was Exhibit No. 3.2 to the registrant's Form S-1 filed with the Securities and Exchange Commission on June 23, 2000 and is incorporated herein by this reference)

4.2(1

)

Bylaws of the Company (which was Exhibit 3.4 to the registrant's Form S-1 filed with the Securities and Exchange Committee on June 23, 2000 and is incorporated herein by this reference)

4.3(1

)

Rights Agreement, dated as of February 13, 2003, between Discovery Partners International, Inc. and American Stock Transfer & Trust Company, which includes the form of Certificate of Designation for the Series A junior participating preferred stock as Exhibit A, the form of Rights Certificate as Exhibit B and the Summary of Rights to Purchase Series A Preferred Stock as Exhibit C (which was Exhibit No. 4.2 to the registrant's Report on Form 8-K filed with the Securities and Exchange Committee on February 24, 2003 and is incorporated herein by this reference)

5.1

 

Opinion of Cooley Godward LLP

10.1(1

)

Second Amended and Restated Investors' Rights Agreement among us and the investors listed on Schedule A thereto, dated April 28, 2000, as amended. (which was Exhibit 10.2 to the registrant's Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on July 26, 2000 and is incorporated herein by this reference.)

10.2(1

)

Standstill Agreement between us and Axys Pharmaceuticals, Inc., dated April 28, 2000. (which was Exhibit 10.12 to the registrant's Registration Statement No. 333-36638 on Form S-1 filed with the Securities and Exchange Commission on May 9, 2000 and is incorporated herein by this reference.)

23.1(1

)

Consent of Ernst & Young LLP, Independent Auditors

24.1(1

)

Power of Attorney (included on signature page)

(1)
Previously filed.



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EXPLANATORY NOTE
PART II INFORMATION NOT REQUIRED IN PROSPECTUS
SIGNATURES
POWER OF ATTORNEY
INDEX TO EXHIBITS