Exhibit 10.39 LEASE AMENDMENT DATED: MARCH 3, 2003 BETWEEN: PACIFIC REALTY ASSOCIATES, L.P., a Delaware limited partnership LANDLORD AND: EXELIXIS PLANT SCIENCES, INC., a wholly owned subsidiary of Exelixis, Inc., a Delaware corporation TENANT Pacific Realty Associates, L.P., a Delaware limited partnership, as Landlord, and American Show Management, Inc. as Original Tenant, entered into a written lease dated October 4, 1995, consisting of approximately 11,059 square feet of office and warehouse space located in Building C, PacTrust Business Center, 16160 S.W. Upper Boones Ferry Road, Portland, Oregon 97224. By Lease Amendment dated June 3, 1996, the Lease was amended. By Assignment and Modification of Lease, dated November 7, 1997, Original Tenant assigned the Lease to Agritope, Inc. By Lease Amendment dated September 9, 1999, Agritope, Inc. leased an additional approximately 6,801 square feet of office and warehouse space. Agritope, Inc.'s leased area now totals approximately 17,860 total square feet of office and warehouse space (hereinafter referred to as the "Premises"). By facsimile dated November 5, 2002, Agritope, Inc. notified Landlord that it had been acquired by Exelixis, Inc. effective December 8, 2000, and changed its name to Exelixis Plant Sciences, Inc., a wholly owned subsidiary of Exelixis, Inc. (hereinafter referred to as "Tenant"). Such documents are hereinafter jointly referred to as "the Lease." The Lease expires February 28, 2003. Tenant now wishes to extend the term of the Lease. NOW, THEREFORE, the parties agree as follows: 1. The term of the Lease shall be extended for an additional thirty-six (36) months commencing March 1, 2003 and continuing through February 28, 2006. 2. Commencing March 1, 2003 and continuing through the extended term, Tenant shall pay base rent according to the following schedule: BASE RENT PERIOD PER MONTH - --------------------------------------- ---------- March 1, 2003 through February 29, 2004 $16,610.00 - --------------------------------------- ---------- March 1, 2004 through February 28, 2005 $17,146.00 - --------------------------------------- ---------- March 1, 2005 through February 28, 2006 $17,681.00 - --------------------------------------- ---------- 3. Except as expressly modified hereby, all terms of the Lease shall remain in full force and effect and shall continue through the extended term. IN WITNESS WHEREOF, the parties hereto have executed this Agreement on the respective dates set opposite their signatures below, but this Agreement on behalf of such party shall be deemed to have been dated as of the date first above written. LANDLORD: PACIFIC REALTY ASSOCIATES, L.P., a Delaware limited partnership By: PacTrust Realty, Inc., a Delaware corporation, its General Partner Date: November 14, 2002 By: /s/ Sam K. Briggs Sam K. Briggs Vice President TENANT: EXELIXIS PLANT SCIENCES, INC., a wholly owned subsidiary of Exelixis, Inc., a Delaware corporation Date: November 14, 2002 By: /s/ Matthew G. Kramer Name: Matthew G. Kramer Title: General Manager