UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, DC 20549 AMENDMENT NO.1 TO FORM 10-Q (MARK ONE) [X] QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 For the quarterly period ended: JUNE 30, 2001 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: 0-30235 EXELIXIS, INC. (Exact name of registrant as specified in its charter) Delaware 04-3257395 (State or other jurisdiction of (I.R.S. Employer incorporation or organization) Identification Number) 170 Harbor Way P.O. Box 511 South San Francisco, CA 94083 (Address of principal executive offices, including zip code) (650) 837-7000 (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 such reports), and (2) has been subject to such filing requirements for the past 90 days: Yes [X] No [ ] As of July 31, 2001, there were 49,161,649 shares of the registrant's common stock outstanding. EXPLANATORY NOTE Exelixis, Inc. is filing this Amendment No. 1 to Form 10-Q as an exhibit-only filing. Exelixis is refiling Exhibit 10.28, Collaboration Agreement, dated May 22, 2001, by and between Exelixis, Inc. and Protein Design Labs, Inc., and confidential treatment has been requested for certain portions of such exhibit. SIGNATURE Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this amendment to report to be signed on its behalf by the undersigned, thereunto duly authorized. Date: September 17, 2001 EXELIXIS, INC. /s/ Glen Y. Sato ------------------- Glen Y. Sato Chief Financial Officer, Vice President of Legal Affairs and Secretary (Principal Financial and Accounting Officer) INDEX TO EXHIBITS Exhibit Number Description of Document ------ ------------------------- 2.1 Share Exchange and Assignment Agreement, dated April 23, 2001, by and among Exelixis, Inc. and the Artemis stockholders named therein. (1) 3.1 Amended and Restated Certificate of Incorporation (2) 3.2 Amended and Restated Bylaws (2) 4.1 Specimen Common Stock Certificate (2) 4.2* Form of Convertible Promissory Note, dated May 22, by and between Exelixis, Inc. and Protein Design Labs, Inc. 4.3* Form of Note Purchase Agreement, dated May 22, by and between Exelixis, Inc. and Protein Design Labs, Inc. 10.28** Collaboration Agreement, dated May 22, 2001, by and between Exelixis, Inc. and Protein Design Labs, Inc. -------------------------------------------------------------------------------- (1) Filed with Exelixis' Item 2 Current Report on Form 8-K filed on May 15, 2001 and incorporated herein by reference. (2) Filed with Exelixis' Registration Statement on Form S-1, as amended (No. 333-96335), declared effective by the Securities and Exchange Commission on April 10, 2000, and incorporated herein by reference. * Previously filed. ** Filed herewith, and confidential treatment requested for certain portions of this exhibit.