Exhibit 10.1

Amendment No. 2 to Note Purchase Agreement
This AMENDMENT No. 2, dated as of August 1, 2013 (this “Amendment”), to the Note
Purchase Agreement, dated as of June 2, 2010, as amended by that certain Consent
and Amendment, dated as of August 6, 2012 (as the same may from time to time be
further amended, modified, supplemented or restated, the “Agreement”), by and
among Exelixis, Inc., a Delaware corporation (the “Borrower”), and those
purchasers set forth on the signature page hereof (individually, a “Purchaser”
and together, the “Purchasers” and, collectively with the Borrower, the
“Parties”). Capitalized terms used herein and not otherwise defined shall have
the meaning given to such terms in the Agreement.
W I T N E S S E T H:
WHEREAS, on July 2, 2010, the Purchasers purchased $124,000,000 aggregate
principal amount of secured convertible notes from the Borrower; and
WHEREAS, the Borrower has requested that the Purchasers amend certain provisions
of the Agreement and the Security Agreement and the Purchasers have agreed to
amend certain provisions of the Agreement and the Security Agreement, but only
to the extent, in accordance with the terms set forth below.
NOW, THEREFORE, in consideration of the mutual agreements set forth herein, the
Purchasers and the Borrower agree as follows:
1.Amendments to the Agreement. The Agreement is hereby amended as follows:
(a)Section 1.1 of the Agreement is hereby amended by replacing the definition of
“Development/Commercialization Revenue” with the following:
“Development/Commercialization Revenue” means, with respect to any fiscal year
of the Borrower, (a) all cash consideration actually received by the Borrower
and its Subsidiaries from any Person, other than the Borrower or any of its
Subsidiaries (other than cash consideration actually received by a non-United
States Person from a United States Person), during such fiscal year relating to
(i) upfront payments pursuant to any Development/Commercialization Agreements
entered into after the Closing Date, and (ii) milestone, profit share and
royalty payments pursuant to any Development/Commercialization Agreements, and
(b) any cash actually received by the Borrower and its Subsidiaries from any
Person, other than the Borrower or any of its Subsidiaries (other than cash
actually received by a non-United States Person from a United States Person),
during such fiscal year from the monetization of any non-cash consideration
relating to payments described in clauses (i) and (ii) above; provided, in each
case, any payments received by the Borrower or any of its Subsidiaries in
respect of the expenses of sponsored research and any other expenses and capital
expenditures incurred by the Borrower or any of its Subsidiaries and reimbursed
pursuant to any Development Commercialization Agreement shall be excluded from
the definition of Development/Commercialization Revenue.
(b)Section 5.2(c) is amended to add the following new clause (vii):

--------------------------------------------------------------------------------

“(vii) prepayments of the Convertible Notes with, or effected by conversions
into or exchanges for, Common Stock, together with cash payments in an aggregate
amount not to exceed $25,000,000.”
2.Amendments to the Security Agreement. The Security Agreement is hereby amended
by adding the following provision to the end of Section 1(b):
Furthermore, notwithstanding anything to the contrary in Section 1(a) above, the
Collateral shall not include voting equity interests in a Foreign Subsidiary or
Foreign Subsidiary Holding Company in excess of 65% of the total voting equity
interests in such Subsidiary. For purposes hereof, “Foreign Subsidiary” means
any Subsidiary that is not organized under the laws of a jurisdiction of the
United States, and “Foreign Subsidiary Holding Company” means any Subsidiary if
all of the assets of such Subsidiary (other than de minimis cash and assets
required to operate) consist of equity interests in a Foreign Subsidiary (such
voting equity interests excluded from the Collateral, the “Excluded Foreign
Equity”). For the avoidance of doubt, to the extent the Secured Party has any
security interests in Excluded Foreign Equity, such security interests are
hereby released.
3.Counterparts; Effectiveness. This Amendment may be executed in several
counterparts, and by each Party on separate counterparts, each of which shall be
deemed an original, but all of which together shall constitute one and the same
agreement. This Amendment shall become effective upon the execution hereof by
the Borrower and the Purchasers.
4.Governing Law. This Amendment shall be governed by and construed in accordance
with the laws of the State of New York, without giving effect to the conflicts
of laws principles thereof other than Sections 5-1401 and 5-1402 of the General
Obligations Law of such State.
5.Effect of Amendment. Except as amended by this Amendment, each of the
Agreement and the Security Agreement remains in full force and effect. For the
avoidance of doubt, this Amendment shall be deemed to be a Finance Document as
defined in the Agreement.
[Signature Page Follows]
 

--------------------------------------------------------------------------------

IN WITNESS WHEREOF, the undersigned Purchasers and the Borrower have caused this
Amendment to be duly executed as of the date first written
above.                    
BORROWER:
PURCHASERS:
EXELIXIS, INC.
DEERFIELD PRIVATE DESIGN FUND, L.P.
 
 
 
 
 
 
By:
Deerfield Mgmt, L.P., its General
Partner
By:
/s/ Frank Karbe
By:
J.E. Flynn Capital LLC, its General Partner
Name:
Frank Karbe
By:
/s/ James E. Flynn
Title:
Executive Vice President and Chief Financial Officer
Name:
James E. Flynn
 
 
Its:
President
 
 
 
 
 
DEERFIELD PRIVATE DESIGN
INTERNATIONAL, L.P.
 
 
 
 
 
 
By:
Deerfield Mgmt, L.P., its General
Partner
 
 
By:
J.E. Flynn Capital LLC, its General Partner
 
 
By:
/s/ James E. Flynn
 
 
Name:
James E. Flynn
 
 
Its:
President