Document:

Prepared by R.R. Donnelley Financial -- EX-4.2

 Exhibit 4.2 

REGISTRATION RIGHTS AGREEMENT 

REGISTRATION RIGHTS AGREEMENT (this “Agreement”), dated as of January 22, 2014, by and between EXELIXIS, INC., a Delaware corporation
(the “Company”), and Deerfield Partners, L.P., Delaware limited partnership, and Deerfield International Master Fund, L.P., a limited partnership organized under the laws of the British Virgin Islands (individually, a
“Lender” and together, the “Lenders”). 
 WHEREAS: 

A. In connection with the Third Amendment to a Note Purchase Agreement by and among the parties hereto, Deerfield Private Design Fund, L.P., a Delaware
limited partnership and Deerfield Private Design International, L.P., a limited partnership organized under the laws of the British Virgin Islands (the “Note Purchase Agreement”), the Company has issued to the Lenders warrants in the
amounts described in the Note Purchase Agreement (the “Warrants”), with each of the Warrants exercisable for shares of the Company’s common stock, par value $0.001 per share (the “Common Stock”), each upon the terms and
conditions and subject to the limitations and conditions set forth in the Warrants; and 
 B. To induce the Lenders to execute and deliver the Note Purchase
Agreement, the Company has agreed to provide certain registration rights under the Securities Act of 1933, as amended, and the rules and regulations thereunder, or any similar successor statute (collectively, the “Securities Act”), and
applicable state securities laws. 
 NOW, THEREFORE, In consideration of the premises and the mutual covenants contained herein and other good and
valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the Company and the Lenders hereby agree as follows: 
 1.
DEFINITIONS. 
 a. As used in this Agreement, the following terms shall have the following meanings: 

(i) “Additional Filing Deadline” means, with respect to any Registration Statements that may be required pursuant to Section 2(a)(ii),
(a) the first date or time that such Registrable Securities may then be included in a Registration Statement if such Registration Statement is required because the SEC shall have notified the Company in writing that certain Registrable
Securities were not eligible for inclusion on a previously filed Registration Statement, or (b) if such additional Registration Statement is required for a reason other than as described in (a) above, the thirtieth (30th) day following the date on which the Company first knows, or reasonably should have known, that such additional Registration Statement is required; provided, however, if the Additional Filing
Deadline would otherwise fall more than 45 days, but less than 91 days, after the end of the Company’s most recent fiscal year and the Company is unable to comply with the Additional Filing Deadline solely as a result of the unavailability of
audited financial statements for such fiscal year, the Additional Filing Deadline shall be extended until the first business day following the earlier to occur of (a) the deadline (without regard to any extensions that may be permitted by Rule
12b-25 under the Exchange Act) for filing by the Company of an annual report on Form 10-K containing such financial statements with the SEC and (b) the date on which the Company files an annual report on Form 10-K containing such financial
statements with the SEC. 
 (ii) “Additional Registration Deadline” means, with respect to any additional Registration Statements that may be
required to be filed pursuant to Section 2(a)(ii), (a) the thirtieth (30th) day following the first date or time that such Registrable Securities may then be included in a
Registration Statement if such Registration Statement is required because the SEC shall have notified the Company in writing that certain Registrable Securities were not eligible for inclusion on a previously filed Registration Statement, or
(b) if such additional Registration Statement is required for a reason other than as described in (a) above, the sixtieth (60th) day following the date on which the Company first knows,
or reasonably should have known, that such additional Registration Statement(s) is required; provided, however, if the applicable Additional Filing Deadline is extended due to the proviso contained in Section 1(a)(i) above, then such Additional
Registration Deadline shall be extended until the thirtieth (30th)  

 
following the Additional Filing Deadline, as so extended, and provided, further, that if, following the filing date but before the date that the additional Registration Statement is declared
effective by the SEC, the Company is unable to file a pre-effective amendment to the additional Registration Statement that is required in order to cause such additional Registration Statement to become effective because such amendment would
otherwise be filed more than 45 days, but less than 91 days, after the end of the Company’s last fiscal year and the audited financial statement for such year are unavailable, the Additional Registration Deadline shall be the date that is the
later of (a) thirty (30) days after the earlier of (1) the deadline (without regard to any extensions that may be permitted by Rule 12b-25 under the Exchange Act) for filing by the Company of an annual report on Form 10-K containing
such financial statements with the SEC and (2) the date on which the Company files an annual report on Form 10-K containing such financial statements with the SEC, and (b) thirty (30) days after the Registration Statement is filed.

 (iii) “Buyer” means each Lender and any permitted transferee or assignee who agrees to become bound by the provisions of this Agreement in
accordance with Section 10 hereof. 
 (iv) “Initial Filing Deadline” shall mean a date that is the later of (a) thirty (30) calendar
days following the date hereof and (b) the first business day after the earlier of (1) the deadline (without regard to any extension that may be permitted by Rule 12b-25 under the Exchange Act) for filing by the Company of an annual report on Form
10-K for the year ended December 27, 2013, and (2) the date on which the Company files an annual report on Form 10-K for the year ended December 27, 2013. 

(v) “Initial Registration Deadline” shall mean the date that is thirty (30) days after the Initial Filing Deadline. 

(vi) “Initial Registration Statement” means the Registration Statement required to be filed under Section 2(a)(i) hereof. 

(vii) “Person” means and includes any natural person, individual, partnership, joint venture, corporation, trust, limited liability company,
limited company, joint stock company, unincorporated organization, government entity or any political subdivision or agency thereof, or any other entity. 

(viii) “Register,” “Registered,” and “Registration” refer to a registration effected by preparing and filing a Registration
Statement or Statements in compliance with the Securities Act and pursuant to Rule 415 under the Securities Act or any successor rule providing for offering securities on a continuous basis, and the declaration or ordering of effectiveness of such
Registration Statement by the United States Securities and Exchange Commission (the “SEC”). 
 (ix) “Registrable Securities” means
(a) any shares of Common Stock (the “Warrant Shares”) issued or issuable upon exercise of the Warrants (without giving effect to any limitations on exercise set forth in the Warrants), including pursuant to a Cash Exercise or a
Cashless Exercise (each as defined in the Warrants), (b) any shares of capital stock issued or issuable as a dividend or other distribution on or in exchange for or otherwise with respect to any of the foregoing and (c) any securities
issued or issuable upon any stock split, recapitalization or similar event with respect to the foregoing; provided, however, that no such securities shall be deemed Registrable Securities for purposes of this Agreement to the extent that such
securities (A) have been sold to the public under a Registration or pursuant to Rule 144 under the Securities Act; (B) have been sold, transferred or otherwise disposed of by a Person in a transaction in which its rights under this
Agreement were not validly assigned pursuant to Section 10 hereof or (C) may be immediately sold to the public without registration or restriction (including without limitation as to volume by each holder thereof) under the Securities Act.

 (x) “Registration Statement(s)” means a registration statement(s) of the Company under the Securities Act required to be filed hereunder. 

  
 2 

 2. REGISTRATION. 

a. MANDATORY REGISTRATION. 
 (i) The Company shall prepare
and, on or prior to the Initial Filing Deadline file with the SEC, the Initial Registration Statement on Form S-3 (or, if Form S-3 is not then available, on such form of Registration Statement as is then available to effect a registration of the
Registrable Securities, subject to the consent of the Buyers, which consent will not be unreasonably withheld) covering the resale of 1,000,000 shares of Common Stock representing the Warrant Shares (the “Initial Registration Shares”),
which Registration Statement, to the extent allowable under the Securities Act and the rules and regulations promulgated thereunder (including Rule 416), shall state that such Registration Statement also covers such indeterminate number of shares of
Common Stock as may become issuable upon exercise of or otherwise pursuant to the Warrants to prevent dilution resulting from stock splits, stock dividends or similar transactions. The number of shares of Common Stock initially included in such
Initial Registration Statement shall be without regard to any limitation on a Buyer’s ability to exercise the Warrants. The Initial Registration Statement (and each amendment or supplement thereto, and each request for acceleration of
effectiveness thereof) shall be provided to each Buyer and its counsel prior to its filing or other submission. 
 (ii) If for any reason the SEC does not
permit all of the Initial Registration Shares to be included in the Registration Statement filed pursuant to Section 2(a)(i) above, or for any other reason any Registrable Securities are not then included in a Registration Statement filed under
this Agreement, then the Company shall prepare, and, as soon as practicable but in no event later than the Additional Filing Deadline, file with the SEC an additional Registration Statement covering the resale of all Registrable Securities not
already covered by an existing and effective Registration Statement for an offering to be made on a continuous basis pursuant to Rule 415. 
 b.
PIGGY-BACK REGISTRATIONS. If, at any time prior to the expiration of the Registration Period (as hereinafter defined), the resale of any Registrable Securities (other than any indeterminate number thereof issuable pursuant to the Warrant other
than pursuant to a Cash Exercise or Cashless Exercise) is not otherwise registered pursuant to an effective Registration Statement and the Company shall determine to file with the SEC a Registration Statement relating to an offering for its own
account or the account of others under the Securities Act of any of its equity securities (other than on Form S-4 or Form S-8 or their then equivalents relating to equity securities to be issued solely in connection with any acquisition of any
entity or business or equity securities issuable in connection with stock option or other employee benefit plans) (a “Piggyback Eligible Registration Statement”), the Company shall send to each Buyer written notice of such determination
and, if within fifteen (15) days after the effective date of such notice, a Buyer shall so request in writing, the Company shall include in such Piggyback Eligible Registration Statement all or any part of the Registrable Securities then
outstanding and not otherwise registered pursuant to an effective Registration Statement, that such Buyer requests to be registered, except that if, in connection with any underwritten public offering for the account of the Company, the managing
underwriter(s) thereof shall impose a limitation on the number of Registrable Securities which may be included in the Piggyback Eligible Registration Statement because, in such underwriter(s)’ judgment, marketing or other factors dictate such
limitation is necessary to facilitate public distribution, then the Company shall be obligated to include in such Piggyback Eligible Registration Statement only such limited portion of the Registrable Securities with respect to which a Buyer has
requested inclusion hereunder as the underwriter shall permit; 
 PROVIDED, HOWEVER, that the Company shall not exclude any Registrable Securities
unless the Company has first excluded all outstanding securities, the holders of which are not entitled by contract to inclusion of such securities in such Registration Statement or are not entitled to pro rata inclusion with the Registrable
Securities; and 
 PROVIDED, FURTHER, HOWEVER, that, after giving effect to the immediately preceding proviso, any exclusion of Registrable
Securities shall be made pro rata with holders of other securities having the contractual right to include such securities in the Piggyback Eligible Registration Statement other than holders of securities entitled to inclusion of their securities in
such Piggyback Eligible Registration Statement by reason of demand registration rights. No right to registration of Registrable Securities under this Section 2(b) shall be construed to limit any registration required under Section 2(a)
hereof. If an offering in connection with which a Buyer is entitled to registration under this Section 2(b) is an underwritten offering, then a Buyer shall, unless otherwise agreed by the Company, offer and sell such Registrable Securities in
an underwritten offering using the same underwriter or underwriters and, subject to the provisions of this Agreement and the underwriting agreement in such offering, on the same terms and conditions as other shares of Common Stock included in such
underwritten offering (including, without limitation, execution of an agreement with the managing underwriter or agent limiting the sale or distribution such Buyer may make of shares of Common Stock or any securities convertible or exchangeable or
exercisable for such shares of the Company, except as part of such registration). Notwithstanding anything to the 

  
 3 

 
contrary set forth herein, the registration rights of the Buyers pursuant to this Section 2(b) shall only be available to the extent that the Buyer holds Registrable Securities and the
Initial Registration Shares are not registered for resale or issuance pursuant to Section 2(a) in accordance with the terms of this Agreement at the time that the Company files a Piggyback Eligible Registration Statement. 

3. OBLIGATIONS OF THE COMPANY. In connection with the registration of the Registrable Securities, the Company shall have the following obligations:

 a. The Company shall (i) prepare and file with the SEC the Registration Statement(s) required pursuant to Section 2(a) above and thereafter use
reasonable best efforts to cause such Registration Statements relating to Registrable Securities to become effective prior to the Initial Registration Deadline or Additional Registration Deadline, as the case may be, and (ii) subject to
Section 3(q) hereof, shall use commercially reasonable efforts to keep each such Registration Statement current and effective pursuant to Rule 415 at all times until such date as the Registrable Securities registered thereunder cease to be
Registrable Securities (the “Registration Period”), which Registration Statement(s) (including any amendments or supplements thereto and prospectuses contained therein), except for information provided by a Buyer or any transferee of a
Buyer pursuant to Section 4(a), shall not contain any untrue statement of a material fact or omit to state a material fact required to be stated therein, or necessary to make the statements therein not misleading. 

b. Subject to Section 3(q) hereof, the Company shall prepare and file with the SEC such amendments (including post-effective amendments) and supplements
to each Registration Statement and the prospectus used in connection with each Registration Statement as may be necessary to keep each Registration Statement effective at all times during the Registration Period, and, during such period, comply with
the provisions of the Securities Act with respect to the disposition of all Registrable Securities of the Company covered by each Registration Statement until the earlier of (i) such time as all of such Registrable Securities have been disposed
of in accordance with the intended methods of disposition by the seller or sellers thereof as set forth in each Registration Statement, and (ii) the Registrable Securities registered thereunder cease to be Registrable Securities. 

c. The Company shall furnish or otherwise make available to each Buyer and its legal counsel (i) promptly after the same is prepared and publicly
distributed, filed with the SEC, or received by the Company, one copy of each Registration Statement and any amendment thereto, each preliminary prospectus and prospectus and each amendment or supplement thereto, and, in the case of a Registration
Statement referred to in Section 2(a), each letter written by or on behalf of the Company to the SEC or the staff of the SEC, and each item of correspondence from the SEC or the staff of the SEC, in each case relating to such Registration
Statement (other than any portion of any thereof which contains information for which the Company has sought or intends to seek confidential treatment), and (ii) such number of copies of a prospectus, including a preliminary prospectus, and all
amendments and supplements thereto and such other documents as a Buyer may reasonably request in order to facilitate the disposition of the Registrable Securities owned by a Buyer. The Company will promptly notify each Buyer by facsimile of the
effectiveness of each Registration Statement or any post-effective amendment. The Company will promptly respond to any and all comments received from the SEC, with a view towards causing each Registration Statement or any amendment thereto to be
declared effective by the SEC as soon as practicable and shall file an acceleration request as soon as practicable, but no later than three (3) business days, following the resolution or clearance of all SEC comments or, if applicable,
following notification by the SEC that any such Registration Statement or any amendment thereto will not be subject to review. 
 d. The Company shall use
commercially reasonable efforts to (i) register and qualify, in any jurisdiction where registration and/or qualification is required, the Registrable Securities covered by the Registration Statements under such other securities or “blue
sky” laws of such jurisdictions in the United States as a Buyer shall reasonably request, (ii) prepare and file in those jurisdictions such amendments (including post-effective amendments) and supplements to such registrations and
qualifications as may be necessary to maintain the effectiveness thereof during the Registration Period, (iii) take such other actions as may be necessary to maintain such registrations and qualifications in effect at all times during the
Registration Period, and (iv) take all other actions reasonably necessary or advisable to qualify the Registrable Securities for sale in such jurisdictions, provided, however, that the Company shall not be required in connection
therewith or as a condition thereto to (A) qualify to do business in any jurisdiction where it would not otherwise be required to qualify but for this Section 3(d), (B) subject itself to general taxation in any such jurisdiction, or
(C) file a general consent to service of process in any such jurisdiction. 

  
 4 

 e. Subject to Section 3(q) hereof, as promptly as practicable after becoming aware of such event, the
Company shall notify each Buyer who holds Registrable Securities of the happening of any event, of which the Company has knowledge, as a result of which the prospectus included in any Registration Statement, as then in effect, includes an untrue
statement of a material fact or omits to state a material fact required to be stated therein or necessary to make the statements therein not misleading, and use its commercially reasonable efforts promptly to prepare a supplement or amendment to any
Registration Statement to correct such untrue statement or omission, and deliver such number of copies of such supplement or amendment to each Buyer as such Buyer may reasonably request. 

f. The Company shall use commercially reasonable efforts to prevent the issuance of any stop order or other suspension of effectiveness of any Registration
Statement, and, if such an order is issued, to obtain the withdrawal of such order at the earliest possible moment and to notify each Buyer who holds Registrable Securities being sold (or, in the event of an underwritten offering, the managing
underwriters) of the issuance of such order and the resolution thereof. 
 g. The Company shall permit a single firm of counsel designated by the Buyers to
review such Registration Statement and all amendments and supplements thereto (as well as all requests for acceleration or effectiveness thereof), at Buyers’ own cost, a reasonable period of time prior to their filing with the SEC (not less
than five (5) business days but not more than eight (8) business days) and use commercially reasonable efforts to reflect in such documents any comments as such counsel may reasonably propose (so long as such comments are provided to the
Company at least (2) business days prior to the expected filing date) and will not request acceleration of such Registration Statement without prior notice to such counsel; provided that the Company shall make the final decision as to the form
and content of each such document. 
 h. The Company shall hold in confidence and not make any disclosure of information concerning a Buyer provided to the
Company unless (i) disclosure of such information is necessary to comply with federal or state securities laws or the rules of any securities exchange or trading market on which the Company’s securities are then listed or traded,
(ii) the disclosure of such information is necessary to avoid or correct a misstatement or omission in any Registration Statement, (iii) the release of such information is ordered pursuant to a subpoena or other order from a court or
governmental body of competent jurisdiction, or (iv) such information has been made generally available to the public other than by disclosure in violation of this or any other agreement. The Company agrees that it shall, upon learning that
disclosure of such information concerning a Buyer is sought in or by a court or governmental body of competent jurisdiction or through other means, give prompt notice to such Buyer prior to making such disclosure, and allow such Buyer, at its
expense, to undertake appropriate action to prevent disclosure of, or to obtain a protective order for, such information. 
 i. The Company shall use
commercially reasonable efforts to cause all the Registrable Securities covered by each Registration Statement to be listed on each securities exchange on which securities of the same class or series issued by the Company are then listed, if any, if
the listing of such Registrable Securities is then permitted under the rules of such exchange, and, if listed on a national exchange, to arrange for at least two market makers to register with the Financial Industry Regulatory Authority, Inc.
(“FINRA”) as such with respect to such Registrable Securities. 
 j. The Company shall provide a transfer agent and registrar, which may be a
single entity, for the Registrable Securities not later than the effective date of the initial Registration Statement. 
 k. The Company shall cooperate
with each Buyer who holds Registrable Securities being offered and the managing underwriter or underwriters as reasonably requested by them with respect to an applicable Registration Statement, if any, to facilitate the timely preparation and
delivery of certificates (not bearing any restrictive legends) representing Registrable Securities to be offered pursuant to such Registration Statement and enable such certificates to be in such denominations or amounts, as the case may be, as the
managing underwriter or underwriters, if any, or a Buyer may reasonably request and registered in such names as the managing underwriter or underwriters, if any, or a 

  
 5 

 
Buyer may request, and, within three (3) business days after a Registration Statement which includes Registrable Securities is ordered effective by the SEC, the Company shall deliver, and
shall cause legal counsel selected by the Company to deliver, to the transfer agent for the Registrable Securities (with copies to each Buyer) an appropriate instruction and an opinion of such counsel in the form required by the transfer agent in
order to issue such Registrable Securities free of restrictive legends upon the resale of such Registrable Securities pursuant to such Registration Statement. 

l. At the reasonable request of a Buyer, the Company shall prepare and file with the SEC such amendments (including post-effective amendments) and supplements
to a Registration Statement and any prospectus used in connection with the Registration Statement as may be necessary in order to change the plan of distribution set forth in such Registration Statement. 

m. The Company shall not, and shall not agree to, allow the holders of any securities of the Company, other than holders of the Registrable Securities, to
include any of their securities in any Registration Statement under Section 2(a) hereof or any amendment or supplement thereto under Section 3(b) hereof without the consent of the Buyers. In addition, the Company shall not offer any
securities for its own account or the account of others in any Registration Statement under Section 2(a) hereof or any amendment or supplement thereto under Section 3(b) hereof without the consent of the Buyers. 

n. The Company shall take all other reasonable actions necessary to expedite and facilitate disposition by the Buyers of Registrable Securities pursuant to a
Registration Statement. 
 o. The Company shall use commercially reasonable efforts to comply with all applicable laws related to a Registration Statement
and offering and sale of securities and all applicable rules and regulations of governmental authorities in connection therewith (including without limitation the Securities Act and the Exchange Act and the rules and regulations promulgated by the
SEC). 
 p. If required by the Financial Industry Regulatory Authority, Inc. Corporate Financing Department, the Company shall promptly effect a filing with
the FINRA pursuant to FINRA Rule 2710 with respect to the public offering contemplated by resales of securities under the Registration Statement (an “Issuer Filing”), and pay the filing fee required by such Issuer Filing. The Company shall
use commercially reasonable efforts to pursue the Issuer Filing until the FINRA issues a letter confirming that it does not object to the terms of the offering contemplated by the Registration Statement. 

q. Notwithstanding anything to the contrary herein, at any time after the Registration Statement has been declared effective by the SEC, the Company may delay
or suspend the effectiveness of any Registration Statement or the use of any prospectus forming a part of the Registration Statement, in its sole discretion, due to the non-disclosure of material, non-public information concerning Company the
disclosure of which at the time is not in its best interest, in the good faith opinion of the Company (a “Grace Period”); provided, that the Company shall promptly notify each Buyer in writing of the existence of a Grace Period in
conformity with the provisions of this Section 3(q) and the date on which the Grace Period will begin (such notice, a “Commencement Notice”); and, provided further, that no Grace Period shall exceed 45 days, and such Grace
Periods shall not exceed an aggregate total of 90 days during any 12-month period. For purposes of determining the length of a Grace Period above, the Grace Period shall begin on and include the date specified by the Company in the Commencement
Notice and shall end on and include the date each Buyer receives written notice of the termination of the Grace Period by the Company (which notice may be contained in the Commencement Notice). The provisions of Sections 3(a)(ii), 3(b) and 3(e)
hereof shall not be applicable during any Grace Period. Upon expiration of the Grace Period, the Company shall again be bound by Sections 3(a)(ii), 3(b) and 3(e) with respect to the information giving rise thereto unless such material, non-public
information is no longer applicable. 
 r. Notwithstanding anything to the contrary herein, a delay in the effectiveness of the Initial Registration
Statement caused solely by the filing of a request for confidential treatment shall not be deemed a breach of the Company’s obligations set forth herein and in such event the Initial Registration Deadline shall be deemed extended to the date
that is ten business days after the date the SEC agrees to allow confidential treatment pursuant to such request or the date such request is withdrawn by the Company, as applicable. 

  
 6 

 4. OBLIGATIONS OF THE BUYER. In connection with the registration of the Registrable Securities, each Buyer
shall have the following obligations: 
 a. It shall be a condition precedent to the obligations of the Company to complete a Registration pursuant to this
Agreement with respect to the Registrable Securities of a Buyer that such Buyer shall furnish to the Company such information regarding itself, the Registrable Securities held by it and the intended method of disposition of the Registrable
Securities held by it as shall be reasonably required to effect the registration of such Registrable Securities and shall execute such documents in connection with such registration as the Company may reasonably request. At least five
(5) business days prior to the first anticipated filing date of a Registration Statement under which Registrable Securities will be registered, the Company shall notify each Buyer of the information the Company requires from such Buyer. Any
such information shall not contain any untrue statement of a material fact or omit to state a material fact required to be stated therein, or necessary to make the statements therein not misleading. A Buyer must provide such information to the
Company at least two (2) business days prior to the first anticipated filing date of such Registration Statement if such Buyer elects to have any Registrable Securities included in the Registration Statement. 

b. Each Buyer, by the Buyer’s acceptance of the Registrable Securities, agrees to cooperate with the Company as reasonably requested by the Company in
connection with the preparation and filing of each Registration Statement hereunder, unless the Buyer has notified the Company in writing of the Buyer’s election to exclude all of the Buyer’s Registrable Securities from such Registration
Statement. 
 c. In the event of an underwritten offering pursuant to Section 2(b) in which any Registrable Securities are to be included, each Buyer
agrees to enter into and perform such Buyer’s obligations under an underwriting agreement, in usual and customary form, including, without limitation, customary indemnification and contribution obligations, with the managing underwriter of such
offering and take such other actions as are reasonably required in order to expedite or facilitate the disposition of the Registrable Securities, unless the Buyer has notified the Company in writing of the Buyer’s election to exclude all of the
Buyer’s Registrable Securities from such Registration Statement. 
 d. Each Buyer agrees that, upon receipt of any notice from the Company of the
happening of any event of the kind described in Sections 3(e), 3(f) or 3(q), the Buyer will immediately discontinue disposition of Registrable Securities pursuant to the Registration Statement covering such Registrable Securities until the
Buyer’s receipt of the copies of the supplemented or amended prospectus contemplated by Section 3(e) or 3(f) or notice from the Company of the termination of the Grace Period, and, if so directed by the Company, the Buyer shall deliver to
the Company (at the expense of the Company) or destroy (and deliver to the Company a certificate of destruction) all copies in the Buyer’s possession, of the prospectus covering such Registrable Securities current at the time of receipt of such
notice. 
 e. Each Buyer agrees that it will not effect any disposition or other transfer of the Registrable Securities that would constitute a sale within
the meaning of the Securities Act other than transactions exempt from the registration requirements of the Securities Act or pursuant to, and as contemplated in, a Registration Statement, and that it will promptly notify the Company of any material
changes in the information set forth in a Registration Statement furnished by or regarding such Buyer or its plan of distribution other than changes in the number of shares beneficially owned. 

5. REGISTRATION FAILURE. In the event of a Registration Failure (as defined in the Warrants), the Buyer shall be entitled to Failure Payments (as
defined in the Warrants) and such other rights as set forth in the Warrants. 
 6. EXPENSES OF REGISTRATION. All expenses of the Company incurred in
connection with registrations, filings or qualifications pursuant to Sections 2 and 3, including, without limitation, all registration, listing and qualification fees, printers and accounting fees and the fees and disbursements of counsel for the
Company, shall be 

  
 7 

 
borne by the Company. All expenses of the Buyers incurred in connection with registrations, filings or qualifications pursuant to Sections 2 and 3, including, without limitation, underwriting
discounts and commissions and legal expenses incurred by any Buyer for review of any Registration Statement, shall be borne by the applicable Buyer. 

7. INDEMNIFICATION. In the event any Registrable Securities are included in a Registration Statement under this Agreement: 

a. The Company will indemnify, hold harmless and defend (i) each Buyer, (ii) the directors, officers, partners, managers, members, employees, agents
and each person who controls each Buyer within the meaning of the Securities Act or the Exchange Act, if any, (iii) any underwriter (as defined in the Securities Act) for each Buyer in connection with an underwritten offering pursuant to
Section 2(b) hereof, and (iv) the directors, officers, partners, managers, members, employees, agents and each person who controls any such underwriter within the meaning of the Securities Act or the Exchange Act, if any (each, an
“Indemnified Person”), against any joint or several losses, claims, damages, liabilities or expenses (collectively, together with actions, proceedings or inquiries by any regulatory or self-regulatory organization, whether commenced or
threatened, in respect thereof, “Claims”) to which any of them may become subject insofar as such Claims arise out of or are based upon: (i) any untrue statement or alleged untrue statement of a material fact in a Registration
Statement or the omission or alleged omission to state therein a material fact required to be stated or necessary to make the statements therein not misleading; (ii) any untrue statement or alleged untrue statement of a material fact contained
in any preliminary prospectus if used prior to the effective date of such Registration Statement, or contained in the final prospectus (as amended or supplemented, if the Company files any amendment thereof or supplement thereto with the SEC) or the
omission or alleged omission to state therein any material fact necessary to make the statements made therein, in light of the circumstances under which the statements therein were made, not misleading; or (iii) any violation or alleged
violation by the Company of the Securities Act, the Exchange Act, any other law, including, without limitation, any state securities law, or any rule or regulation thereunder relating to the offer or sale of the Registrable Securities (the matters
in the foregoing clauses (i) through (iii) being, collectively, “Violations”). The Company shall reimburse the Indemnified Person, promptly as such expenses are incurred and are due and payable, for any reasonable legal fees or
other reasonable expenses incurred by them in connection with investigating or defending any such Claim. Notwithstanding anything to the contrary contained herein, the indemnification agreement contained in this Section 7(a): (A) shall not
apply to a Claim arising out of or based upon a Violation to the extent that such Violation occurs in reliance upon and in conformity with information furnished in writing to the Company by any Indemnified Person for use in connection with the
preparation of such Registration Statement or any such amendment thereof or supplement thereto; (B) with respect to any preliminary prospectus, shall not inure to the benefit of any such Person from whom the Person asserting any such Claim
purchased the Registrable Securities that are the subject thereof (or to the benefit of any Person controlling such Person) if the untrue statement or omission of material fact contained in the preliminary prospectus was corrected in the prospectus,
as then amended or supplemented, if such prospectus was timely made available by the Company pursuant to Section 3(d), and the Indemnified Person was promptly advised in writing not to use the incorrect prospectus prior to the use giving rise
to a violation and such Indemnified Person, notwithstanding such advice, used it or failed to deliver the correct prospectus as required by the Securities Act and such correct prospectus was timely made available pursuant to Section 3(d);
(C) shall not be available to the extent such Claim is based on a failure of the Indemnified Person to deliver or to cause to be delivered the prospectus made available by the Company, including a corrected prospectus, if such prospectus or
corrected prospectus was timely made available by the Company pursuant to Section 3(d); and (D) shall not apply to amounts paid in settlement of any Claim if such settlement is effected without the prior written consent of the Company,
which consent shall not be unreasonably withheld or delayed. Such indemnity shall remain in full force and effect regardless of any investigation made by or on behalf of the Indemnified Person and shall survive the transfer of the Registrable
Securities by a Buyer pursuant to Section 10 and shall be binding on any transferee. 
 b. Promptly after receipt by an Indemnified Person under this
Section 7 of notice of the commencement of any action (including any governmental action), such Indemnified Person shall, if a Claim in respect thereof is to be made against the Company under this Section 7, deliver to the Company a
written notice of the commencement thereof, and the Company shall have the right to participate in, and, to the extent the Company so desires, to assume control of the defense thereof with counsel mutually satisfactory to the Company and the
Indemnified Person, as the case may be. 

  
 8 

 PROVIDED, HOWEVER, that an Indemnified Person shall have the right to retain its own counsel with the
reasonable fees and expenses to be paid by the Company, if, in the reasonable opinion of counsel for a Buyer, the representation by such counsel of the Indemnified Person and the Company would be inappropriate due to actual or potential differing
interests between such Indemnified Person and any other party represented by such counsel in such proceeding. The Company shall pay for only one separate legal counsel for the Indemnified Persons, and such legal counsel shall be selected by the
Buyers. The failure to deliver written notice to the Company within a reasonable time of the commencement of any such action shall not relieve the Company of any liability to the Indemnified Person under this Section 7, except to the extent
that the Company is actually prejudiced in its ability to defend such action. The indemnification required by this Section 7 shall be made by periodic payments of the amount thereof during the course of the investigation or defense, as such
expense, loss, damage or liability is incurred and is due and payable. 
 c. Each Buyer will indemnify, hold harmless and defend (i) the Company, and
(ii) the directors, officers, partners, managers, members, employees, agents and each person who controls the Company within the meaning of the Securities Act or the Exchange Act, if any (each, a “Company Indemnified Person”), against
any joint or several losses, claims, damages, liabilities or expenses (collectively, together with actions, proceedings or inquiries by any regulatory or self-regulatory organization, whether commenced or threatened, in respect thereof,
“Indemnity Claims”) to which any of them may become subject insofar as such Indemnity Claims arise out of or are based upon any Violation which occurs due to the inclusion by the Company in a Registration Statement of false or misleading
information about such Buyer, where such information was furnished in writing to the Company by such Buyer expressly for inclusion in such Registration Statement. Such Buyer shall reimburse the Company Indemnified Person, promptly as such expenses
are incurred and are due and payable, for any reasonable legal fees or other reasonable expenses incurred by them in connection with investigating or defending any such Claim, provided, however, that the indemnity agreement contained in this
Section 7(c) and the agreement with respect to contribution contained in Section 8 shall not apply to amounts paid in settlement of any Claim if such settlement is effected without the prior written consent of the Buyer and which consent
shall not be unreasonably withheld or delayed; provided, further, however, that the Buyer shall be liable under this Section 7(c) for only that amount of a Claim as does not exceed the net amount of proceeds received by the Buyer as a result of
the sale of Registrable Securities pursuant to such Registration Statement. Such indemnity shall remain in full force and effect regardless of any investigation made by or on behalf of the Company Indemnified Person. Notwithstanding anything to the
contrary contained herein, the indemnification agreement contained in this Section 7(c) with respect to any preliminary prospectus shall not inure to the benefit of any Company Indemnified Person if the untrue statement or omission of material
fact contained in the preliminary prospectus was corrected on a timely basis in the prospectus, as then amended or supplemented. 
 d. Promptly after
receipt by a Company Indemnified Person under this Section 7 of notice of the commencement of any action (including any governmental action), such Company Indemnified Person shall, if a Claim in respect thereof is to be made against a Buyer
under this Section 7, deliver to such Buyer a written notice of the commencement thereof, and such Buyer shall have the right to participate in, and, to the extent the Buyer so desires, to assume control of the defense thereof with counsel
mutually satisfactory to the Buyer and the Company Indemnified Person, as the case may be. 
 PROVIDED, HOWEVER, that a Company Indemnified Person
shall have the right to retain its own counsel with the reasonable fees and expenses to be paid by the applicable Buyer, if, in the reasonable opinion of counsel for the Company, the representation by such counsel of the Company Indemnified Person
and such Buyer would be inappropriate due to actual or potential differing interests between such Company Indemnified Person and any other party represented by such counsel in such proceeding. A Buyer shall pay for only one separate legal counsel
for the Company Indemnified Persons, and such legal counsel shall be selected by Company. The failure to deliver written notice to a Buyer within a reasonable time of the commencement of any such action shall not relieve the Buyer of any liability
to the Company Indemnified Person under this Section 7, except to the extent that the Buyer is actually prejudiced in its ability to defend such action. The indemnification required by this Section 7 shall be made by periodic payments of
the amount thereof during the course of the investigation or defense, as such expense, loss, damage or liability is incurred and is due and payable. 

  
 9 

 8. CONTRIBUTION. To the extent any indemnification by the Company or a Buyer is prohibited or limited by
law, each of the Company and each Buyer agrees to make the maximum contribution with respect to any amounts for which it would otherwise be liable under Section 7 to the fullest extent permitted by law, based upon a comparative fault standard,
that (i) no Person that is guilty of fraudulent misrepresentation (within the meaning Section 11(f) of the Securities Act) in connection with such sale shall be entitled to contribution from any Person who was not guilty of fraudulent
misrepresentation; and (ii) contribution by a Buyer shall be limited in amount to the net amount of proceeds received by the Buyer from the sale of such Registrable Securities pursuant to a Registration Statement. 

9. REPORTS UNDER THE 1934 ACT. With a view to making available to the Buyers the benefits of Rule 144 promulgated under the Securities Act or any other
similar rule or regulation of the SEC that may at any time permit the Buyers to sell securities of the Company to the public without registration the Company agrees to: 

a. make and keep public information available, as those terms are understood and defined in Rule 144; 

b. file with the SEC in a timely manner all reports and other documents required of the Company under the Securities Act and the Exchange Act so long as the
Company remains subject to such requirements and the filing of such reports and other documents is required for the applicable provisions of Rule 144; and 

c. furnish to the Buyers so long as the Buyers own Registrable Securities, promptly upon request, (i) a written statement by the Company that it has
complied with the reporting requirements of the Securities Act and the Exchange Act as required for applicable provisions of Rule 144, (ii) a copy of the most recent annual or quarterly report of the Company and such other reports and documents
so filed by the Company, and (iii) such other information as may be reasonably requested to permit the Buyers to sell such securities pursuant to Rule 144 without registration. 

Each Buyer shall at all times comply with the restrictions on transfer contained in Section 8 of the Warrant, which provisions are hereby incorporated by
reference and made a part hereof. 
 10. ASSIGNMENT OF REGISTRATION RIGHTS. The rights under this Agreement shall be automatically assignable by each
Buyer to any transferee of all or any portion of the Registrable Securities if: (i) the Buyer agrees in writing with the transferee or assignee to assign such rights, and a copy of such agreement is furnished to the Company within a reasonable
time after such assignment, (ii) the Company is, within a reasonable time after such transfer or assignment, furnished with written notice of (a) the name and address of such transferee or assignee, and (b) the securities with respect
to which such registration rights are being transferred or assigned, and (iii) at or before the time the Company receives the written notice contemplated by clause (ii) of this sentence, the transferee or assignee agrees in writing with
the Company to be bound by all of the provisions contained herein. In the event that a Buyer transfers all or any portion of its Registrable Securities pursuant to this Section, the Company shall have at least ten (10) business days following
the receipt of such notice to file any amendments or supplements necessary to keep a Registration Statement current and effective pursuant to Rule 415, and the commencement date of any Event of Failure (as defined in the Warrants) under the Warrants
caused thereby will be extended by ten (10) business days. 
 11. AMENDMENT OF REGISTRATION RIGHTS. Provisions of this Agreement may be amended
and the observance thereof may be waived (either generally or in a particular instance and either retroactively or prospectively), with written consent of the Company and the holders of a majority in interest of then-outstanding Registrable
Securities. Any amendment or waiver effected in accordance with this Section 11 shall be binding upon the Buyers and the Company. 
 12. TERMINATION
OF RIGHTS AND OBLIGATIONS. The obligations of the Company pursuant to the terms of this Agreement, other than the obligations set forth in Sections 6, 7, 8 and 13, shall terminate on the date upon which all Registrable Securities held by a
Holder or issuable to a holder upon exercise of Warrants cease to be Registrable Securities.  

  
 10 

 13. MISCELLANEOUS. 

a. A person or entity is deemed to be a holder of Registrable Securities whenever such person or entity owns of record or beneficially through a “street
name” holder such Registrable Securities. If the Company receives conflicting instructions, notices or elections from two or more persons or entities with respect to the same Registrable Securities, the Company shall act upon the basis of
instructions, notice or election received from the registered owner of such Registrable Securities. 
 b. Any notices required or permitted to be given
under the terms hereof shall be in writing and shall be deemed given only if sent by certified or registered mail (return receipt requested) or delivered personally or by courier (including a recognized overnight delivery service) or by facsimile
and shall be effective five days after being placed in the mail, if mailed by regular United States mail, or upon receipt, if delivered personally or by courier (including a recognized overnight delivery service) or by facsimile, in each case
addressed to a party. The addresses for such communications shall be: 
 If to the Company: 

Exelixis, Inc. 
 210 East Grand Ave. 

South San Francisco, CA 94080 
 Fax: (650) 837-7951 

Attn: Executive Vice President and General Counsel 
 With copy
to: 
 Cooley LLP 
 101 California Street 

San Francisco, CA 94111 
 Fax: (415) 693-2222 

Attn: Gian-Michele a Marca, Esq. 
 If to a Buyer: 

c/o Deerfield Mgmt, L.P. 
 780 Third Avenue, 37th Floor 
 New York, New York 10017 

Fax: (212) 599-1248 
 Attn: Alexander Karnal 

With a copy to: 
 Katten Muchin Rosenman LLP 

575 Madison Avenue 
 New York, New York 10022 

Fax: (212) 940-8776 
 Attn: Mark I. Fisher, Esq. 

          Elliot Press, Esq. 

Each party shall provide notice to the other party of any change in address. 

  
 11 

 c. Failure of any party to exercise any right or remedy under this Agreement or otherwise, or delay by a party in
exercising such right or remedy, shall not operate as a waiver thereof. 
 d. Governing Law. All questions concerning the construction, validity,
enforcement and interpretation of this Agreement shall be governed by and construed and enforced in accordance with the internal laws of the State of New York, without regard to the principles of conflicts of law thereof. Each party agrees that all
legal proceedings concerning the interpretations, enforcement and defense of the transactions contemplated by this Agreement (whether brought against a party hereto or its respective affiliates, directors, officers, shareholders, employees or
agents) shall be commenced exclusively in either the state and federal courts sitting in the City of New York or City of San Francisco, California. Each party hereby irrevocably submits to the exclusive jurisdiction of the state and federal courts
sitting in the City of New York, borough of Manhattan and the City of San Francisco, California for the adjudication of any dispute hereunder or in connection herewith or with any transaction contemplated hereby or discussed herein, and hereby
irrevocably waives, and agrees not to assert in any suit, action or proceeding, any claim that it is not personally subject to the jurisdiction of any such court, that such suit, action or proceeding is improper or is an inconvenient venue for such
proceeding. Each party hereby irrevocably waives personal service of process and consents to process being served in any such suit, action or proceeding by mailing a copy thereof via registered or certified mail or overnight delivery (with evidence
of delivery) to such party at the address in effect for notices to it under this Agreement and agrees that such service shall constitute good and sufficient service of process and notice thereof. Nothing contained herein shall be deemed to limit in
any way any right to serve process in any other manner permitted by law. The parties hereby waive all rights to a trial by jury. If either party shall commence an action or proceeding to enforce any provision of this Agreement, then the prevailing
party in such action or proceeding shall be reimbursed by the other party for its reasonable attorneys’ fees and other costs and expenses incurred with the investigation, preparation and prosecution of such action or proceeding. 

e. This Agreement, the Warrants and the Note Purchase Agreement (including all schedules and exhibits thereto) constitute the entire agreement among the
parties hereto with respect to the subject matter hereof and thereof. There are no restrictions, promises, warranties or undertakings, other than those set forth or referred to herein and therein. This Agreement, the Warrants and the Note Purchase
Agreement supersede all prior agreements and understandings among the parties hereto with respect to the subject matter hereof and thereof. 
 f. Subject to
the requirements of Section 10 hereof, this Agreement shall inure to the benefit of and be binding upon the successors and assigns of each of the parties hereto. 

g. The headings in this Agreement are for convenience of reference only and shall not limit or otherwise affect the meaning hereof. 

h. This Agreement may be executed in two or more counterparts, each of which shall be deemed an original but all of which shall constitute one and the same
agreement. This Agreement, once executed by a party, may be delivered to the other party hereto by facsimile transmission of a copy of this Agreement bearing the signature of the party so delivering this Agreement. 

i. Each party shall do and perform, or cause to be done and performed, all such further acts and things, and shall execute and deliver all such other
agreements, certificates, instruments and documents, as the other party may reasonably request in order to carry out the intent and accomplish the purposes of this Agreement and the consummation of the transactions contemplated hereby. 

j. The Company acknowledges that a breach by it of its obligations hereunder will cause irreparable harm to the Buyers by vitiating the intent and purpose of
the transactions contemplated hereby. Accordingly, the Company acknowledges that the remedy at law for breach of its obligations hereunder will be inadequate and agrees, in the event of a breach or threatened breach by the Company of any of the
provisions hereunder, that the Buyers shall be entitled, in addition to all other available remedies in law or in equity, to an injunction or injunctions to prevent or cure breaches of the provisions of this Agreement and to enforce specifically the
terms and provisions hereof, without the necessity of showing economic loss and without any bond or other security being required. 

  
 12 

 k. The language used in this Agreement will be deemed to be the language chosen by the parties to express their
mutual intent, and no rules of strict construction will be applied against any party. 
 l. In the event that any provision of this Agreement is invalid or
unenforceable under any applicable statute or rule of law, then such provision shall be deemed inoperative to the extent that it may conflict therewith and shall be deemed modified to conform with such statute or rule of law. Any provision hereof
which may prove invalid or unenforceable under any law shall not affect the validity or enforceability of any other provision hereof. 
 m. In the event a
Buyer shall sell or otherwise transfer any of such holder’s Registrable Securities, each transferee shall be allocated a pro rata portion of the number of Registrable Securities included in a Registration Statement for such transferor. 

n. There shall be no oral modifications or amendments to this Agreement. This Agreement may be modified or amended only in writing. 

[Remainder of page left intentionally blank] 

[Signature page follows] 

  
 13 

 IN WITNESS WHEREOF, each of the undersigned Buyers and the Company have caused this Agreement to be duly executed
as of the date first written above. 
  

									
	COMPANY:	 		 	BUYER:
	EXELIXIS, INC.	 		 	DEERFIELD PARTNERS, L.P.
					
	By:	 	  /s/ Michael M. Morrissey
	 		 	By:	 	Deerfield Mgmt, L.P., General Partner
	Name:	 	Michael M. Morrissey	 		 	By:	 	J.E. Flynn Capital, LLC, General Partner
	Title:	 	President and Chief Executive Officer	 		 		 	
		 		 		 	By:	 	  /s/ David J. Clark

		 		 		 	Name:	 	 David J. Clark

		 		 		 	Title:	 	Authorized Signatory
			
		 		 	DEERFIELD INTERNATIONAL MASTER FUND, L.P.
					
		 		 		 	By:	 	Deerfield Mgmt, L.P., General Partner
		 		 		 	By:	 	J.E. Flynn Capital, LLC, General Partner
					
		 		 		 	By:	 	  /s/ David J. Clark

		 		 		 	Name:	 	 David J. Clark

		 		 		 	Title:	 	 Authorized SignatoryPrepared by R.R. Donnelley Financial -- EX-10.1

 Exhibit 10.1 

THIRD AMENDMENT TO NOTE PURCHASE AGREEMENT 

THIS THIRD AMENDMENT TO NOTE PURCHASE AGREEMENT (this “Amendment”) is dated as of January 22, 2014 by and among
EXELIXIS, INC., a Delaware corporation (“Borrower”), DEERFIELD PRIVATE DESIGN FUND, L.P., a Delaware limited partnership (“DPDF”), DEERFIELD PRIVATE DESIGN INTERNATIONAL, L.P., a limited partnership organized under
the laws of the British Virgin Islands (together with DPDF, collectively, referred to as “Purchasers”), DEERFIELD PARTNERS, L.P., a Delaware limited partnership (“DPLP”), and DEERFIELD INTERNATIONAL MASTER FUND,
L.P., a limited partnership organized under the laws of the British Virgin Islands (together with DPLP, collectively, the “Assignees”). 

W I T N E S S E T H: 
 WHEREAS,
Borrower and Purchasers have entered into that certain Note Purchase Agreement dated as of June 2, 2010 (as the same may be amended, modified, restated or otherwise supplemented from time to time, the “Purchase Agreement”);

 WHEREAS, Borrower has requested that Purchasers and Assignees amend the Purchase Agreement in certain respects; and 

WHEREAS, Purchasers and Assignees are willing to amend the Purchase Agreement on the terms and conditions set forth in this Amendment. 

NOW, THEREFORE, in consideration of the mutual agreements, provisions and covenants contained herein, the parties agree as follows: 

1. Defined Terms. Capitalized terms used herein which are defined in the Purchase Agreement, unless otherwise defined herein, shall
have the meanings ascribed to them in the Purchase Agreement. 

 2. Amendments to Purchase Agreement. 

Upon the satisfaction of the conditions set forth in Section 3 to this Amendment the Purchase Agreement shall be amended as follows: 

a. The definition of “Customary Subordination Terms” in Section 1.1 of the Purchase Agreement is hereby deleted in its entirety
and the following is inserted in substitution therefor: 
 “Customary Subordination Terms” means, with respect to any
subordinated Indebtedness, that (1) no payment in respect of such Indebtedness may be made if (a) an Event of Default pursuant to Section 5.5(a) shall have occurred and is continuing, including as a result of the delivery of an
Acceleration Notice (as defined in Section 5.5), until such Acceleration Notice is rescinded or the Notes have been paid in full or (b) any other Event of Default shall have occurred and be continuing and the Purchasers shall have sent to
the Borrower a notice of default (a “Payment Blockage Notice”); provided that no more than one Payment Blockage Notice may be sent during any 365 day period and payments in respect of such Indebtedness may resume upon the earliest to occur
of (i) the date on which such default is cured or waived in writing by Purchasers or Assignees (ii) 91 days after the date the Notes are paid in full, (iii) the date 179 days after the date on which the Payment Blockage Notice is
received, and (iv) the date the Payment Blockage Notice is rescinded, and (2), in the case of any Indebtedness specified in clause (d) of the definition of Permitted Indebtedness, such Indebtedness matures on or after, does not require any
scheduled amortization or other scheduled payments of principal and is not prepaid by Borrower (except as permitted under Section 5.2(c)), prior to January 1, 2019 (it being understood that any provision requiring an offer to purchase such
Indebtedness as a result of a change of control or asset sale shall not violate the foregoing restriction, provided that the Obligations are concurrently repaid in full). 

b. The definition of “Development/Commercialization Revenue” in Section 1.1 of the Purchase Agreement is hereby deleted in its
entirety and the following is inserted in substitution therefor: 
 ““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, during such fiscal
year relating to (i) upfront payments pursuant to any Development/Commercialization Agreements, 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, 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, (x) 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, (y) any revenue derived from Product Sales, and (z) any proceeds from an Intellectual Property Sale shall, in each case, be excluded from the
definition of Development/Commercialization Revenue.” 

  
 2 

 c. The definition of “Discount Factor” in Section 1.1 of the Purchase Agreement is
hereby deleted in its entirety. 
 d. The definition of Excluded Taxes is hereby deleted in its entirety and the following is inserted in
substitution therefor: 
 “Excluded Taxes” means (i) all income taxes, minimum or alternative minimum income taxes,
withholding taxes imposed on gross amounts, any tax determined based upon income, capital gains, gross income, sales, net profits, windfall profits or similar items, franchise taxes (or any other tax measured by capital, capital stock or net worth),
gross receipts taxes, branch profits taxes, margin taxes (or any other taxes imposed on or measured by net income, or imposed in lieu of net income) in any jurisdiction by any Government Authority (or political subdivision or taxing authority
thereof) other than, solely with respect to a Purchaser that is not a “United States person” within the meaning of Section 7701(a)(30) of the Code, any Taxes imposed by any U.S. federal, U.S. state or U.S. local Government Authority
in connection with any payments received (whether in cash or stock) under this Agreement by such Purchaser or with the execution and delivery of, and the performance of its obligations under, this Agreement, other than Taxes imposed with respect to
FATCA and (ii) any withholding Tax imposed by the United States under FATCA as a direct result of such Purchaser’s or Assignee’s failure to deliver the required IRS forms certifying as to its exemption from withholding under
FATCA”. 
 e. The definition of “Excluded Transaction” in Section 1.1 of the Purchase Agreement is hereby deleted in its
entirety and the following is inserted in substitution therefor: 
 “Excluded Transaction” means any of the
following transactions: 
 (a) the entering into any collaborative arrangement, licensing agreement, joint venture or
partnership providing for the research, development or commercial exploitation of compounds, products or services that provides for the payments received therefrom or the Borrower’s income or profits to be shared with another Person, including,
without limitation, (1) the grant, to an entity engaged in the pharmaceutical or biotechnology industry, of a license or option to obtain a license to any of the Borrower’s Intellectual Property or other assets, provided that the Borrower
or a wholly owned Subsidiary of the Borrower (and not any third party or any of the Borrower’s stockholders) directly receives from such entity all consideration paid or payable by such entity in consideration of

  
 3 

 
such grant (other than any payments made by such third party in satisfaction of obligations of the Borrower or its wholly-owned Subsidiaries), which consideration may, but need not, include
(without limitation) upfront, milestone, royalty and profit-sharing payments, and (2) the grant of a license or option to obtain a license to, or the sale or other transfer of, the Borrower’s Intellectual Property or other assets to any
entity that intends to research and develop or commercialize products or services covered by such Intellectual Property or embodying or arising from such other assets, whether directly or through the Borrower or another entity, provided that the
Borrower or a wholly owned Subsidiary of the Borrower (and not any third party or any of the Borrower’s stockholders) retains the right or has the obligation to reacquire such Intellectual Property or other assets at a price no more than an
amount that reasonably reflects the value of such assets or Intellectual Property or to terminate such license or option; 

(b) the incurrence, grant or existence of, or any sale or transfer of any assets in connection with, any Permitted Lien; or

 (c) Product Sales; 

provided, however, notwithstanding any provision of this definition to the contrary, an Intellectual Property Sale shall not
constitute an Excluded Transaction.” 
 f. Subsection (b) of the definition of “Major Transaction” in Section 1.1
of the Purchase Agreement is hereby deleted in its entirety and the following is inserted in substitution therefor: 

“(b)(i) the sale or transfer of assets in one transaction or a series of related transactions for a purchase price
(excluding any consideration allocable to any Excluded Transaction or Intellectual Property Sale relating to cabozantinib) (“Aggregate Consideration”) of more than (i) $400 million or (ii) 50% of Borrower’s Market
Capitalization (as defined below). “Market Capitalization” means the product of (x) the number of issued and outstanding shares of Common Stock as of the Trading Day (as defined in Section 2.9) immediately preceding the date of
the execution of the definitive agreement relating to such transaction or transactions, multiplied by (y) the per share closing price of the Common Stock on such Trading Day.” 

  
 4 

 g. The definition of “Maturity Date” in Section 1.1 of the Purchase Agreement is
hereby amended by adding the following proviso to the end thereof: 
 “; provided, however, that in the
event of an Extension, “Maturity Date” means July 1, 2018.” 
 h. The definition of “Notes” in
Section 1.1 of the Purchase Agreement is hereby deleted in its entirety and the following is inserted in substitution therefor: 

““Notes” means the secured convertible notes purchased by the Purchasers pursuant to Section 2.1
hereof or assigned to the Assignees in the forms attached hereto as Exhibit A-1 and Exhibit A-2, as amended, modified, restated or supplemented from time to time.” 

i. The definition of “Optional Prepayment Price” in Section 1.1 of the Purchase Agreement is hereby deleted in its entirety.

 j. The definition of “Permitted Indebtedness” in Section 1.1 of the Purchase Agreement is hereby deleted in its entirety
and the following shall be deemed inserted in substitution therefor, provided that if Borrower’s right to make an Extension Election shall have expired or Borrower has previously irrevocably waived, in writing, Borrower’s right to make an
Extension Election, then the definition of “Permitted Indebtedness” shall revert to the definition in Section 1.1 of the Purchase Agreement, without giving effect to this Section 2(j): 

““Permitted Indebtedness” means: (a) Indebtedness of Borrower in favor of the Purchasers arising
under the Notes and this Agreement, (b) Indebtedness existing as of the date hereof and disclosed on Exhibit B hereof, (c) Indebtedness to trade creditors incurred in the ordinary course of business, (d) Indebtedness incurred in
connection with and owed to other parties (or one or more Affiliates of the other parties) to, collaboration, licensing, joint venture or partnership arrangements (i) prior to January 22, 2014, or (ii) on or after January 22, 2014 if such
Indebtedness is contractually subject to Customary Subordination Terms or otherwise subordinated to the Obligations by written agreement on terms and conditions acceptable to the Purchasers, (e) Indebtedness in respect of purchase money
financing, capital lease obligations and equipment financing facilities, including without limitation, indebtedness pursuant to that certain Loan and Security Agreement, dated as of May 22, 2002, as amended, supplemented or otherwise modified
from time to time, between the Borrower and Silicon Valley Bank (and any borrowings thereunder converted into term loans), (f) (i) the Convertible Notes and (ii) unsecured Indebtedness consisting of subordinated convertible notes so
long as such notes are contractually subordinated on Customary Subordination Terms or otherwise subordinated to the Obligations by written agreement on terms and conditions acceptable to the Purchasers, (g) Indebtedness incurred to finance
insurance premiums or time-based license or 

  
 5 

 
royalty payments, in each case in the ordinary course of business, (h) Indebtedness in respect of netting services, overdraft protections and other similar and customary services in
connection with deposit accounts, (i) guaranties in the ordinary course of business of the obligations of suppliers, customers and licenses of the Borrower, (j) Indebtedness owed to any Subsidiary subordinated to the Obligations and
evidenced by an intercompany note that includes the subordination provisions set forth on Exhibit D or otherwise subordinated to the Obligations on terms and conditions acceptable to Purchasers, (k) Indebtedness in respect of any and all
interest rate swap transactions, basis swaps, credit derivative transactions, forward interest rate transactions, commodity swaps, commodity options, forward commodity contracts, equity or equity index swaps or options, bond or bond price or bond
index swaps or options or forward bond or forward bond price or forward bond index transactions, interest rate options, forward foreign exchange transactions, interest rate or foreign exchange rate cap, floor or collar transactions, currency swap
transactions, cross-currency rate swap transactions, currency options, spot contracts, or any other similar transactions or any combination of any of the foregoing (including any options to enter into any of the foregoing), in each case in the
ordinary course of business, (l) any Indebtedness the net proceeds of which are used to prepay the Notes, (m) Indebtedness in respect of workers’ compensation claims, self-insurance obligations, indemnities, bankers’ acceptances,
performance and surety bonds, appeal or other similar bonds, in each case in the ordinary course of business, in any such case, any reimbursement obligations in connection therewith, (n) Indebtedness in connection with letter of credit
obligations incurred in the ordinary course of business, (o) Indebtedness arising from agreements providing for indemnification, and (p) extensions, refinancings, replacements and renewals of any items of Permitted Indebtedness, provided
that the principal amounts and premiums, if any, are not increased (plus the amount of any costs and expenses incurred therewith).” 

k. The definition of “Principal Amount” in Section 1.1 of the Purchase Agreement is hereby deleted in its entirety and the
following is inserted in substitution therefor: 
 ““Principal Amount” means, with respect to any Note (or portion
thereof), the principal amount of such Note (or portion thereof) payable at maturity thereof, and with respect to all Notes, means $124,000,000, in each case, less any repayments pursuant to Sections 2.2 and 2.10 hereof, and plus any additional
loans, whether in the form of principal or interest, pursuant to Section 2.10 hereof.” 

  
 6 

 l. Section 1.1 of the Purchase Agreement is hereby amended to add the following additional
defined terms: 
 “Assignees” means collectively, Deerfield Partners, L.P., a Delaware limited partnership,
and Deerfield International Master Fund, L.P., a limited partnership organized under the laws of the British Virgin Islands. 

“Exchange Act” means the United States Securities and Exchange Act of 1934, as amended. 

“Exclusive License” means, with respect to any drug or pharmaceutical product, any license to the Intellectual
Property relating to such drug or pharmaceutical product with a term greater than, or substantially equal to the remaining expected useful life, or, if applicable, patent life of such Intellectual Property (unless terminable prior to such time
without material penalty or premium by the licensor) and which provides for exclusive rights to develop, commercialize, sell, market and promote such drug or product within the United States, Europe and/or Japan; provided that an “Exclusive
License” shall not include (a) any license solely to sell, offer for sale, use, promote and/or distribute any such drug or product on an exclusive basis within any particular geographic region or territory in consideration for sales based
payments to Borrower, (b) any licenses, which may be exclusive, solely to manufacture any such drug or product, and (c) any license solely to manufacture, use, promote, offer for sale and/or sell any authorized generic version of such drug
or product. 
 “Extension” means an extension of the Maturity Date pursuant to Section 2.10. 

“Extension Election” has the meaning given such term in Section 2.10. 

“Election Date” has the meaning given such term in Section 2.10. 

“FATCA” means Sections 1471 through 1474 of the Code, as amended, or any amended or successor version thereof,
any Treasury Regulations or other official interpretations thereof, and any fiscal or regulatory legislation, rules or practices adopted pursuant to any intergovernmental agreement entered into in connection with the implementation of such Sections
of the Code. 
 “Intellectual Property” shall have the meaning provided therefor in the Security Agreement.

  
 7 

 “Intellectual Property Sale” means any sale, assignment, the
grant of any Exclusive License or other transfer of the rights, title or interest of Borrower or any of its Subsidiaries in Intellectual Property as a result of which the Borrower or its Subsidiary transfers all or substantially all of its legal or
economic interests, in the Intellectual Property in a transaction whereby the predominate consideration received for transferred interests in such Intellectual Property is to be received upfront as compared to any retained or reversionary interests
in such Intellectual Property and any rights of the Borrower or any of its Subsidiaries to royalties, milestones, profit sharing and other future payments in respect of such Intellectual Property; provided that an Intellectual Property Sale does not
include (a) the assignment, cancellation, abandonment or other disposition of Intellectual Property that is, in the reasonable judgment of Borrower, no longer economically practicable to maintain or useful for the sale of the applicable drug or
product or in the conduct of the business of Borrower and its Subsidiaries, taken as a whole and which does not have material value, or (b) any license or sublicense that is not an Exclusive License. 

“Prepayment Price” has the meaning given such term in Section 2.2(e). 

“Product Sales” means the sale or distribution by the Borrower or any of its Subsidiaries of drug or
pharmaceutical products in the ordinary course of Borrower’s or such Subsidiary’s business. 

“Registration Rights Agreement” means the Registration Rights Agreement in the form of Exhibit B to the
Third Amendment. 
 “Supplemental Indenture” means that certain First Supplemental Indenture dated as of
August 14, 2012 to the Indenture dated as of August 14, 2012 between Borrower and Wells Fargo Bank, National Association as Trustee with respect to the Convertible Notes. 

“Third Amendment” means the Third Amendment to Note Purchase Agreement dated as of January 22, 2014 among
Borrower, Purchasers and Assignees. 
 “Warrants” shall have the meaning provided therefor in the Third
Amendment. 

  
 8 

 m. Section 2.2 of the Purchase Agreement is deleted in its entirety and substituted by the
following: 
 “(a) Subject to Maximum Annual Prepayment Amount, on or before January 10, 2015, the Borrower shall
prepay a portion of the Principal Amount of the Notes equal to 15% of the Development/Commercialization Revenue actually received by the Borrower during the first three quarters of the previous fiscal year (the “Quarterly Prepayment
Amount”) and from and after an Extension and receipt by Borrower of an Election Notice, Borrower shall, on or before each of January 10, 2016, 2017 and 2018, prepay a portion of the Principal Amount of the Notes in an amount of up to
the Quarterly Prepayment Amount for the applicable previous fiscal year. 
 In the event of receipt of an Election Notice and
subject to the Maximum Annual Prepayment Amount, Borrower shall (i) on or before the thirtieth Trading Day (as such term is defined in Section 2.9(e)) after the Borrower files its Annual Report on Form 10-K for the fiscal year ended
January 2, 2015 and each of the fiscal years ending on or about December 31, 2015, 2016 and 2017, or (ii) if the Borrower is not then required to file reports pursuant to Section 13 or 15(d) of the Exchange Act, on or before each
of January 31, 2015, January 31, 2016, January 31, 2017 and January 31, 2018, as applicable, prepay a portion of the Principal Amount of the Notes equal to the difference between (A) 15% of the
Development/Commercialization Revenue actually received by the Borrower during the previous fiscal year and (B) the Quarterly Prepayment Amount for such previous fiscal year. 

The Borrower shall provide to the Purchasers at least five Business Days notice prior to each such prepayment date the
calculation of such Development/Commercialization Revenue for the relevant fiscal year, together with the basis for such calculation, and shall promptly provide to the Purchasers such information as the Purchasers shall reasonably request to permit
the Purchasers to verify each such calculation. 
 The Principal Amount of the Notes to be prepaid pursuant to this
subsection (a) with respect to any fiscal year shall not exceed the lesser of (i) the sum of the Quarterly Prepayment Amount and any further amounts payable pursuant to the preceding two paragraphs and (ii) $27,500,000 (the
“Maximum Annual Prepayment Amount”). 
 Purchasers shall notify Borrower in writing within five Business
Days of the receipt of such calculation, of their election to require a prepayment and the amount of such prepayment (each, an “Election Notice”). Upon Purchasers’ receipt of each of the prepayments specified in this
Section 2.2(a) (each, a “Mandatory Prepayment Amount”), the Principal Amount shall be reduced by such Mandatory Prepayment Amount. 

  
 9 

 (b) On the Maturity Date, the outstanding Principal Amount of the Notes shall
become due and payable, together with any other accrued and unpaid Obligations. 
 (c) On a Major Transaction Put Date, the
Borrower shall prepay the Notes in full by paying Purchasers simultaneously with the consummation of the Major Transaction an amount equal to the Prepayment Price. 

(d) Prior to any Intellectual Property Sale, Borrower shall notify the Purchasers in writing and, at the Purchaser’s
election, prepay the Principal Amount of the Notes in an amount equal to (i) 100% of the cash proceeds of any Intellectual Property Sale of Intellectual Property relating to cabozantinib, and (ii) 50% of the cash proceeds of any
Intellectual Property Sale of any other Intellectual Property, in each case when and as such cash proceeds are received (including any cash proceeds from any subsequent sale of any non-cash proceeds received from such Intellectual Property Sale) and
net of any fees and expenses and estimated taxes payable in respect of such Intellectual Property Sale. 
 (e) The Borrower
may prepay the Notes by paying to the Purchasers (i) at any time prior to July 1, 2015, (1) the outstanding Principal Amount of the Notes, (2) all accrued and unpaid interest through the date of such prepayment payment,
(3) all interest that would accrue on the Principal Amount from the date of prepayment through the applicable Maturity Date if the outstanding Principal Amount of the Notes as of such date were to remain outstanding through the applicable
Maturity Date, and (4) all other accrued and unpaid Obligations, and (ii) from and after an Extension, (1) an amount equal to 105% of the outstanding Principal Amount of the Notes, (2) all accrued and unpaid interest through the
date of such prepayment payment, and (3), if prior to July 1, 2017, all interest that would accrue on the Principal Amount from the date of prepayment through July 1, 2017 if the outstanding Principal Amount of the Notes as of such date
were to remain outstanding through July 1, 2017, and (4) all other accrued and unpaid Obligations (collectively the “Prepayment Price”).” 

  
 10 

 n. The last full sentence of Section 2.8 of the Purchase Agreement is hereby deleted in its
entirety and the following is inserted in substitution therefor: 
 “Any such interest shall be in addition to any
interest otherwise payable under Section 2.7 or Section 2.10, as applicable, and shall be payable on demand.” 
 o.
Section 2.9 of the Purchase Agreement is hereby amended to delete the reference to the words “Optional Prepayment Amount” where it appears therein and insert in substitution therefor the term “Prepayment Price”. In addition,
from and after an Extension, the maximum number of shares of Common Stock specified in Section 2.9(i) shall be replaced with 33,889,596 shares of Common Stock. 

p. Article II of the Purchase Agreement is hereby amended by adding the following new subsection 2.10 thereto: 

“Section 2.10. Extension of Maturity. Subject to the terms of this Section 2.10, Borrower may, unless
expressly waived in writing by Borrower prior to such date, by written notice to Purchasers prior to March 31, 2015, elect to extend the Maturity Date to July 1, 2018 (“Extension Election” and the date of such Extension
Election, the “Election Date”). 
 In the event of an Extension Election by Borrower, on July 1, 2015:
(i) Borrower shall pay the Prepayment Price less such amount as shall cause the Principal Amount after such payment to be One Hundred Thousand Dollars ($100,000), (ii) Purchasers shall, sell, assign and transfer the Notes, together with
all collateral and security for the Obligations and all rights, title and interest in the Financing Documents to Assignees, for One Hundred Thousand Dollars ($100,000), plus all accrued and unpaid interest, (iii) Assignees shall loan to
Borrower an amount equal to Ninety Nine Million Nine Hundred Thousand Dollars ($99,900,000) (such amounts to be allocated among the Assignees at their own discretion) such that the Principal Amount following such loans equals One Hundred Million
Dollars ($100,000,000), (iv) the Borrower shall execute and deliver to Assignees amended and restated notes in the form of Exhibit A to the Third Amendment in the then outstanding Principal Amount of the Notes after giving effect to such
readvance, in substitution for and replacement of the Notes, and (v) notwithstanding anything to the contrary contained in, and in lieu of Section 2.7, (1) the outstanding Principal Amount of the Notes shall thereafter bear interest
at the rate of fifteen percent (15%) per annum, payable quarterly, in arrears, on each March 31, June 30, September 30 and December 31, with any partial quarterly periods being pro-rated based on a 365 day or 366
day year, as 

	

	

  
 11 

 
applicable, (2) on each such quarterly interest payment date one half of the interest payable on the outstanding Principal Amount of the Notes shall be automatically added to the outstanding
Principal Amount of the Notes and bear interest as provided herein and one half of the interest payable on the outstanding Principal Amount of the Notes shall be payable in cash on each such quarterly interest payment date, and
(3) Section 2.7 shall cease to have any force or effect. For the avoidance of doubt, the transactions contemplated in clauses (i), (ii) and (iii) may occur substantially concurrently and if so directed by Borrower, the Assignees
shall make the advances contemplated under clause (iii) (prior to any repayment under clause (i)) directly to an escrow account in the name of Borrower, subject to a first priority lien in favor of Assignees, to be disbursed by the escrowee to
Purchasers, on behalf of Borrower, pursuant to written escrow instructions from Assignees and Borrower, in payment of the amount due to Purchasers set forth in (i) above. 

In the event Borrower makes an Extension Election, the term of the Warrants shall automatically be extended by two years beyond
their current Ending Date (as defined in the Warrants) and the Exercise Price (as defined in the Warrants) shall be adjusted to the lesser of (i) the Exercise Price as set forth in Section 3(c) of the Third Amendment and (ii) 120% of
the Volume Weighted Average Price of the Common Stock for the ten (10) Trading Days immediately following the Extension Election. 

Purchasers’ and Assignees’ obligation to extend the Maturity Date pursuant to this Section 2.10 is subject to
the following conditions precedent: 
 (1) No Event of Default shall have occurred or be continuing on either the Election
Date or July 1, 2015; 
 (2) As of both the Election Date and July 1, 2015, the representations and warranties of
Borrower contained in this Agreement are (i) in the case of representations and warranties qualified by “materiality,” “Material Adverse Effect” or similar language, true and correct in all respects and (ii) in the case
of all other representations and warranties, true and correct in all material respects, in each case on and as of the date hereof, true and correct after giving effect to the consents, waivers and amendments herein (including with respect to any
particular representations or warranties as contemplated or delivered hereunder), except to the extent that any such representation or warranty relates to a specific date, in which case such representation and warranty shall be true and correct in
all respects or all material respects, as applicable, as of such earlier date; and 

  
 12 

 (3) Borrower shall have executed and delivered to Assignees amended and restated
Notes, in the form of Exhibit A to the Third Amendment. 
 q. Sections 5.4, 5.5 and 5.6 of the Purchase Agreement are hereby amended to
delete the reference to the words “Put Price” wherever they appear therein and insert in substitution therefor the words “Prepayment Price”. 

r. Article III of the Purchase Agreement is hereby amended by adding the following new subsection 3.3(h): 

The Assignees’ receipt of the Warrants will not cause either Purchaser to own, or be treated as owning under the attribution rules of
Section 871(h)(3)(C), 10% or more of the total combined voting power of the stock of Borrower. 
 3. Conditions Precedent. The
effectiveness of this Amendment is subject to the following conditions precedent: 
 a. Delivery of Documents. The following shall
have been delivered to Purchasers, each duly executed and in form and substance satisfactory to Purchasers in their sole discretion: 
  

	 	i.	this Amendment; 

  

	 	ii.	evidence of the due authorization of this Amendment by Borrower’s board of directors; and 

  

	 	iii.	a Registration Rights Agreement in the form of Exhibit B to this Amendment. 

 b.
Performance; No Default. Borrower shall have performed and complied with all agreements and conditions contained in the Purchase Agreement and the other Financing Documents to be performed by or complied with by Borrower prior to the date
hereof in all respects, and, after giving effect to this Amendment, no Event of Default shall exist or be created hereby. 
 c. Delivery
of Warrants. Upon the date of this Amendment, Borrower shall issue to the Assignees Warrants to Purchase, in the aggregate, one million (1,000,000) shares of Common Stock (the “Warrants”) in the form annexed hereto as Exhibit C
containing an initial Exercise Price (as defined in the Warrants) equal to $9.70. Prior to the delivery of Warrants, each Assignee shall provide the Borrower with IRS Form W-9 or the applicable IRS Form W-8 (including all required attachments). 

  
 13 

 All Warrants that are issued pursuant to this Amendment shall be allocated to Assignees in such
ratio as Assignees shall provide the Borrower at any time and from time to time. 
 4. Representations and Warranties. Borrower
hereby represents and warrants to Purchasers and Assignees as follows: 
 a. As of the date hereof, the representations and warranties of
Borrower contained in the Financing Documents are (i) in the case of representations and warranties qualified by “materiality,” “Material Adverse Effect” or similar language, true and correct in all respects and (ii) in
the case of all other representations and warranties, true and correct in all material respects, in each case on and as of the date hereof, except to the extent that any such representation or warranty relates to a specific date, in which case such
representation and warranty shall be true and correct in all respects or all material respects, as applicable, as of such earlier date; 

b. The execution, delivery and performance by Borrower of this Amendment, the Warrants, the Registration Rights Agreement and Amended and
Restated Notes (i) are within Borrower’s corporate powers, (ii) have been duly authorized by all necessary action pursuant to its Organizational Documents, (iii) require no further action by or in respect of, or filing with, any
Government Authority, except for such registrations and filings in connection with the issuance of the shares of Common Stock pursuant to Section 2.9 of the Purchase Agreement or required pursuant to the terms of the Warrants and the
Registration Rights Agreement and (iv) do not violate, conflict with or cause a breach or a default under any provision of applicable law or regulation or of Borrower’s Organizational Documents or of any agreement, judgment, injunction,
order, decree or other instrument binding upon Borrower; 
 c. This Amendment constitutes the valid and binding obligation of Borrower,
enforceable against Borrower in accordance with its terms, except as enforceability may be limited by applicable bankruptcy, insolvency, or similar laws relating to the enforcement of creditor’s rights generally and by general equitable
principles; 
 d. No Event of Default exists; 

e. The Notes, as amended pursuant to this Agreement constitute, and upon (i) any assignment thereof to Assignees, (ii) the making of
a loan pursuant to Section 2.10 of the Purchase Agreement by Assignees in the amount of any principal paid by Borrower on or about the original Maturity Date pursuant to Section 2.10 of the Purchase Agreement, and (iii) the extension
of the Maturity Date as provided in Section 2.10 of the Purchase Agreement, will continue to constitute, Senior Indebtedness as such term is defined in the Supplemental Indenture, and upon any such assignment and loan of repaid principal,
Assignees will be holders 

  
 14 

 
of Senior Indebtedness as to all outstanding amounts (including, without limitation, the amount of such loan) and entitled to all of the rights and benefits to which such a holder is entitled
under the Supplemental Indenture, including, without limitation, the provisions of Article 5 thereof; and 
 f. The Warrants and the shares
of Common Stock issuable upon exercise of the Warrants (the “Warrant Shares”), have been duly authorized and the Warrant Shares when issued, delivered and paid for in accordance with the terms of the Warrants, will have been validly
issued and will be fully paid and nonassessable. There are no preemptive rights or other rights to subscribe for or to purchase, or any restriction upon the voting or transfer of any shares of Common Stock pursuant to the Borrower’s
Organizational Documents or any agreements to which the Borrower or any of its Subsidiaries is a party or by which the Borrower or any of its Subsidiaries is bound. 

5. No Further Amendments; Ratification of Liability. Except as amended hereby, the Purchase Agreement and each of the other Financing
Documents shall remain in full force and effect in accordance with their respective terms. Borrower as debtor, grantor, pledgor, guarantor or assignor, or in any similar capacity in which it has granted Liens or acted as an accommodation party or
guarantor, as the case may be, hereby ratify, confirms and reaffirms its liabilities, their payment and performance obligations (contingent or otherwise) and their agreements under the Purchase Agreement and the other Financing Documents to the
extent such Person is a party thereto, all as amended by this Amendment, and the liens and security interests granted, created and perfected thereby. The Purchasers’ and Assignees’ agreement to the terms of this Amendment or any other
amendment of the Purchase Agreement or any other Financing Document shall not be deemed to establish or create a custom or course of dealing among Borrower, Purchasers, Assignees, or any of them. This Amendment, together with the Warrants and the
Registration Rights Agreement and the other Financing Documents, contains the entire agreement among Borrower, Purchasers and Assignees contemplated by this Amendment. 

6. Release. By execution of this Amendment, Borrower acknowledges and confirms that it does not as of the date hereof have any offsets,
defenses or claims arising out of or relating to this Amendment, the Purchase Agreement or the other Financing Documents against any Purchaser, Assignee, or any of their subsidiaries, affiliates, officers, directors, employees, agents, attorneys,
predecessors, successors or assigns whether asserted or unasserted. To the extent that such offsets, defenses or claims may exist as of the date hereof, Borrower for itself and its successors, assigns, parents, subsidiaries, affiliates,
predecessors, employees, agents, heirs and executors, as applicable (collectively, “Releasors”), releases and forever discharges each Purchaser, Assignee and their subsidiaries, affiliates, officers, directors, employees, agents,
attorneys, predecessors, successors and assigns, both present and former (collectively, the “Purchaser Affiliates”) of and from any and all manner of actions, causes of action, torts, suits, debts, controversies, damages, judgments,
executions, claims and demands whatsoever, asserted 

  
 15 

 
or unasserted, in law or in equity, arising out of or relating to this Amendment, the Purchase Agreement and the other Financing Documents which Releasors ever had or now have against Purchasers,
Assignees and/or Purchaser Affiliates, including, without limitation, any presently existing claim or defense whether or not presently suspected, contemplated or anticipated. 

7. Severability. In case any provision of or obligation under this Amendment shall be invalid, illegal or unenforceable in any
jurisdiction, the validity, legality and enforceability of the remaining provisions or obligations, or of such provision or obligation in any other jurisdiction, shall not in any way be affected or impaired thereby. 

8. Headings. Headings and captions used in this Amendment (including the Exhibits, Schedules and Annexes hereto, if any) are included
for convenience of reference only and shall not be given any substantive effect. 
 9. GOVERNING LAW; SUBMISSION TO JURISDICTION.
THIS AMENDMENT SHALL BE GOVERNED AND CONTROLLED BY THE INTERNAL LAWS OF THE STATE OF NEW YORK AS TO INTERPRETATION, ENFORCEMENT, VALIDITY, CONSTRUCTION, EFFECT, AND IN ALL OTHER RESPECTS, WITHOUT GIVING EFFECT TO THE CONFLICTS OF LAWS PRINCIPLES
THEREOF OTHER THAN SECTION 5/1401 AND 5-1402 OF THE GENERAL OBLIGATIONS LAW OF SUCH STATE. EACH PARTY HEREBY IRREVOCABLY SUBMITS TO THE JURISDICTION OF THE STATE AND FEDERAL COURTS SITTING IN THE CITY OF NEW YORK, BOROUGH OF MANHATTAN OR THE CITY OF
SAN FRANCISCO FOR THE ADJUDICATION OF ANY DISPUTE HEREUNDER OR IN CONNECTION HEREWITH OR WITH ANY TRANSACTION CONTEMPLATED HEREBY OR DISCUSSED HEREIN, AND HEREBY IRREVOCABLY WAIVES, AND AGREES NOT TO ASSERT IN ANY SUIT, ACTION OR OTHER PROCEEDING,
ANY CLAIM THAT IT IS NOT PERSONALLY SUBJECT TO THE JURISDICTION OF ANY SUCH COURT THAT SUCH COURT, ACTION OR PROCEEDING IS IMPROPER OR IS AN INCONVENIENT VENUE FOR SUCH PROCEEDING. FINAL NON-APPEALABLE JUDGMENT AGAINST ANY PARTY IN ANY SUCH ACTION,
SUIT OR OTHER PROCEEDING SHALL BE CONCLUSIVE AND MAY BE ENFORCED IN ANY JURISDICTION BY SUIT ON THE JUDGMENT. NOTHING CONTAINED IN ANY FINANCING DOCUMENT SHALL AFFECT THE RIGHT OF THE PURCHASERS TO COMMENCE LEGAL PROCEEDINGS IN ANY COURT HAVING
JURISDICTION, OR CONCURRENTLY IN MORE THAN ONE JURISDICTION, OR TO SERVE PROCESS, PLEADINGS AND OTHER LEGAL PAPERS UPON THE BORROWER IN ANY MANNER AUTHORIZED BY THE LAWS OF ANY SUCH JURISDICTION. THE BORROWER IRREVOCABLY WAIVES, TO THE FULLEST
EXTENT PERMITTED BY APPLICABLE LAW, ANY OBJECTION WHICH IT MAY NOW OR HEREAFTER HAVE TO THE LAYING OF VENUE OF ANY ACTION, SUIT OR OTHER PROCEEDING ARISING OUT OF OR RELATING TO ANY FINANCING DOCUMENT, BROUGHT IN

  
 16 

 
THE COURTS OF THE STATE OF NEW YORK OR IN THE UNITED STATES DISTRICT COURT FOR THE SOUTHERN DISTRICT OF NEW YORK, AND ANY CLAIM THAT ANY SUCH ACTION, SUIT OR OTHER PROCEEDING BROUGHT IN ANY SUCH
COURT HAS BEEN BROUGHT IN AN INCONVENIENT FORUM. 
 10. WAIVER OF JURY TRIAL. BORROWER, PURCHASERS AND ASSIGNEES HEREBY WAIVE ALL
RIGHTS TO TRIAL BY JURY IN ANY ACTION OR PROCEEDING WHICH PERTAINS DIRECTLY OR INDIRECTLY TO THIS AMENDMENT, ANY OF THE OTHER FINANCING DOCUMENTS, THE OBLIGATIONS, THE COLLATERAL, ANY ALLEGED TORTIOUS CONDUCT BY SUCH OBLIGOR OR LENDER OR WHICH, IN
ANY WAY, DIRECTLY OR INDIRECTLY, ARISES OUT OF OR RELATES TO THE RELATIONSHIP AMONG BORROWER, PURCHASERS AND ASSIGNEES. IN NO EVENT SHALL ANY PARTY BE LIABLE FOR LOST PROFITS OR OTHER SPECIAL, EXEMPLARY, PUNITIVE OR CONSEQUENTIAL DAMAGES. 

11. Notices. The addresses for any notice, request or other communication pursuant to Section 6.1 of the Purchase Agreement are
hereby revised as follows for Borrower and set forth as follows for the Assignees: 
 If to Borrower: 

Exelixis, Inc. 
 210 East Grand
Ave. 
 South San Francisco, CA 94080 

Fax: (650) 837-7951 
 Attn:
Executive Vice President and General Counsel 
 With a courtesy copy to: 

Cooley LLP 
 101 California Street

 San Francisco, CA 94111 

Fax: (415) 693-2222 
 Attn:
Gian-Michele a Marca, Esq. 
 For the Assignees c/o: 

Deerfield Mgmt, L.P. 
 780 Third
Avenue, 37th Floor 
 New York, New York 10017 

Fax: (212) 599-1248 
 Attn:
Alexander Karnal 

  
 17 

 With a courtesy copy to: 

Katten Muchin Rosenman LLP 
 575
Madison Avenue 
 New York, New York 10022 

Fax: (212) 940-8776 
 Attn:
Robert I. Fisher 
 12. Counterparts; Integration. This Amendment may be executed and delivered via facsimile with the same force and
effect as if an original were executed and may be signed in any number of counterparts, each of which shall be an original, with the same effect as if the signatures hereto were upon the same instrument. This Amendment constitutes the entire
agreement and understanding among the parties hereto with respect to the subject matter hereof and supersedes any and all prior agreements and understandings, oral or written, relating to the subject matter hereof. This Amendment shall be considered
part of the Purchase Agreement and shall be a Financing Document for all purposes under the Purchase Agreement and other Financing Documents. 

[Remainder of Page Intentionally Left Blank, signature page follows] 

  
 18 

 IN WITNESS WHEREOF, the parties have executed this Amendment as of the date set forth above. 

 

			
	BORROWER:
	
	EXELIXIS, INC.
		
	By:	 	  /s/ Micheal M. Morrissey

	Name:	 	Micheal M. Morrissey
	Title:	 	President and Chief Executive Officer
	
	PURCHASERS:
	
	DEERFIELD PRIVATE DESIGN FUND, L.P.
		
	By:	 	Deerfield Mgmt, L.P., General Partner
	By:	 	J.E. Flynn Capital, LLC, General Partner
		
	By:	 	  /s/ David J. Clark

	Name:	 	David J. Clark
	Title:	 	Authorized Signatory
	
	DEERFIELD PRIVATE DESIGN INTERNATIONAL, L.P.
		
	By:	 	Deerfield Mgmt, L.P., General Partner
	By:	 	J.E. Flynn Capital, LLC, General Partner
		
	By:	 	  /s/ David J. Clark

	Name:	 	David J. Clark
	Title:	 	Authorized Signatory
	
	ASSIGNEES:
	
	DEERFIELD PARTNERS, L.P.
		
	By:	 	Deerfield Mgmt, L.P., General Partner
	By:	 	J.E. Flynn Capital, LLC, General Partner
		
	By:	 	  /s/ David J. Clark

	Name:	 	David J. Clark
	Title:	 	 Authorized Signatory

  
 19 

			
	DEERFIELD INTERNATIONAL MASTER FUND, L.P.
		
	By:	 	Deerfield Mgmt, L.P., General Partner
	By:	 	J.E. Flynn Capital, LLC, General Partner
		
	By:	 	  /s/ David J. Clark

	Name:	 	David J. Clark
	Title:	 	Authorized Signatory

  
 20 

 Exhibit A 

Form of Amended and Restated Notes 

AMENDED AND RESTATED SECURED CONVERTIBLE NOTE 

THE SECURITY REPRESENTED BY THIS CERTIFICATE HAS NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, OR APPLICABLE STATE SECURITIES LAWS. THIS SECURITY MAY
NOT BE SOLD, TRANSFERRED OR ASSIGNED, PLEDGED, HYPOTHECATED OR OTHERWISE DISPOSED OF IN THE ABSENCE OF AN EFFECTIVE REGISTRATION STATEMENT FOR THE SECURITIES UNDER SAID ACT, OR PURSUANT TO AN EXEMPTION FROM REGISTRATION UNDER SAID ACT INCLUDING,
WITHOUT LIMITATION, PURSUANT TO RULE 144 UNDER SAID ACT. 
 THIS NOTE IS BEING ISSUED WITH ORIGINAL ISSUE DISCOUNT (“OID”). THE
FOLLOWING INFORMATION IS BEING PROVIDED PURSUANT TO TREASURY REGULATION SECTION 1.275-3: 
  

					
	 ISSUE PRICE:
	  	$	            	  
	 AMOUNT OF OID:
	  	$	            	  
	 ISSUE DATE:
	  	 	July 1, 2015	  
	 MATURITY DATE:
	  	 	July 1, 2018	  

 July 1, 2015 

FOR VALUE RECEIVED, EXELIXIS, INC., a Delaware corporation (the “Issuer”), by means of this Amended and Restated
Secured Convertible Note (this “Note”), hereby unconditionally promises to pay to             (the “Holder”), a principal amount equal to
($            ) (or such lesser amount as may be outstanding under this Note as result of prepayments and conversions by the Borrower pursuant to the Note Purchase Agreement (as
defined below)), in lawful money of the United States of America and in immediately available funds, on the dates provided in the Note Purchase Agreement. 

This Note is a “Note” referred to in the Note Purchase Agreement dated as of June 2, 2010 among the Issuer, the Holder
and the other parties thereto (as amended, restated, supplemented or otherwise modified from time to time, the “Note Purchase Agreement”), with respect to the purchase of this Note by the Holder thereunder. Capitalized terms used
herein and not expressly defined in this Note shall have the respective meanings assigned to them in the Note Purchase Agreement. All Obligations of the Issuer under this Note are secured as provided in the Security Agreement. 

This Note shall bear interest on the Principal Amount hereof in the amounts set forth in and pursuant to the provisions of the Note Purchase
Agreement. This Note is subject to the voluntary and mandatory prepayment provisions set forth in the Note Purchase Agreement. 

 The Issuer shall make all payments to the Holder of interest and principal under this Note in the
manner provided in and otherwise in accordance with the Note Purchase Agreement. The principal amount of this Note may be converted into shares of Common Stock as set forth in the Note Purchaser Agreement. On July 1, 2018 and on any Major
Transaction Put Date, the Principal Amount of this Note shall become due and payable. 
 If default is made in the punctual payment of
principal or any other amount under this Note in accordance with the Note Purchase Agreement, or if any other Event of Default has occurred, this Note shall, at the Holder’s option exercised at any time upon or after the occurrence of any such
payment default or other Event of Default and in accordance with the applicable provisions of the Note Purchase Agreement, become immediately due and payable. 

All payments of any kind due to the Holder from the Issuer pursuant to this Note shall be made in the full face amount thereof, other
than Excluded Taxes and Taxes for which the Holder (as a “Purchaser”) is responsible for pursuant to Section 2.5(b) of the Note Purchase Agreement. The Issuer shall pay all and any costs (administrative or otherwise) imposed by
banks, clearing houses, or any other financial institution, in connection with making any payments hereunder, except for any costs imposed by the Holder’s banking institutions. 

The Issuer shall pay all reasonable costs of collection, including, without limitation, all reasonable, documented legal expenses and
attorneys’ fees, paid or incurred by the Holder in collecting and enforcing this Note. 
 The Issuer and every endorser of this Note,
or the obligations represented hereby, expressly waives presentment, protest, demand, notice of dishonor or default, and notice of any kind with respect to this Note and the Note Purchase Agreement or the performance of the obligations under this
Note and/or the Note Purchase Agreement. No renewal or extension of this Note or the Note Purchase Agreement, no release of any Person primarily or secondarily liable on this Note or the Note Purchase Agreement, including the Issuer and any
endorser, no delay in the enforcement of payment of this Note or the Note Purchase Agreement, and no delay or omission in exercising any right or power under this Note or the Note Purchase Agreement shall affect the liability of the Issuer or any
endorser of this Note. 
 No delay or omission by the Holder in exercising any power or right hereunder shall impair such right or power or
be construed to be a waiver of any default, nor shall any single or partial exercise of any power or right hereunder preclude the full exercise thereof or the exercise of any other power or right. The provisions of this Note may be waived or amended
only in a writing signed by the Issuer and the Holder. This Note may be prepaid in whole or in part without premium or penalty, including in shares of Common Stock in accordance with the provisions of the Note Purchase Agreement. 

THIS NOTE, AND ANY RIGHTS OF THE HOLDER ARISING OUT OF OR RELATING TO THIS NOTE, MAY, AT THE OPTION OF THE HOLDER, BE ENFORCED BY THE HOLDER
IN THE COURTS OF THE UNITED STATES OF AMERICA LOCATED IN THE SOUTHERN DISTRICT OF THE STATE OF NEW YORK OR IN ANY OTHER COURTS HAVING JURISDICTION. FOR THE BENEFIT OF THE HOLDER, THE ISSUER HEREBY IRREVOCABLY AGREES THAT ANY LEGAL ACTION, SUIT OR
OTHER 

  
 2 

 
PROCEEDING ARISING OUT OF OR RELATING TO THIS NOTE MAY BE BROUGHT IN THE COURTS OF THE STATE OF NEW YORK OR OF THE UNITED STATES OF AMERICA FOR THE SOUTHERN DISTRICT OF NEW YORK, AND HEREBY
CONSENTS THAT PERSONAL SERVICE OF SUMMONS OR OTHER LEGAL PROCESS MAY BE MADE AS SET FORTH IN SECTION 6.1 OF THE NOTE PURCHASE AGREEMENT, WHICH SERVICE THE ISSUER AGREES SHALL BE SUFFICIENT AND VALID. THE ISSUER HEREBY WAIVES ANY AND ALL RIGHTS TO
DEMAND A TRIAL BY JURY IN ANY ACTION, SUIT OR OTHER PROCEEDING ARISING OUT OF OR RELATING TO THIS NOTE OR THE TRANSACTIONS CONTEMPLATED BY THIS NOTE. 

This Note shall be governed by, and construed in accordance with, the laws of the State of New York applicable to contracts made and to be
performed in such State, without giving effect to the conflicts of laws principles thereof other than Sections 5-1401 and 5-1402 of the General Obligations Law of the State of New York. 

Whenever this Note is held by a noteholder that is not a “United States person” within the meaning of
Section 7701(a)(30) of the Internal Revenue Code of 1986, as amended (the “Code”), then it is the intention of the Issuer and such noteholder that (x) all interest accrued and paid on this Note will qualify for exemption
from United States withholding tax as “portfolio interest” because this Note is an obligation which is in “registered form” within the meaning of Sections 871(h)(2)(B) and 881(c)(2)(B) of the Code and the applicable Treasury
Regulations promulgated thereunder, and (y) as such, all interest accrued and paid on this Note will be exempt from United States information reporting under Sections 6041 and 6049 of the Code and United States backup withholding under
Section 3406 of the Code. The Issuer and the Holder shall reasonably cooperate with one another, and execute and file such forms or other documents, or do or refrain from doing such other acts, as may be required, to secure such exemptions from
United States withholding tax, information reporting, and backup withholding. In furtherance of the foregoing, any Holder, transferee or assignee noteholder that is not a United States person shall represent, warrant and covenant to the Issuer that
(i) such noteholder is not, and will not be as long as any amounts due under this Note have not been paid in full, a “United States person,” within the meaning of Section 7701(a)(30) of the Code; (ii) such noteholder is not,
and will not be as long as any amounts due under this Note have not been paid in full, a person described in Section 881(c)(3) of the Code; (iii) on or prior to the date of transfer or assignment (and on or prior to the date the form
provided pursuant to this clause (iii) is no longer valid) until all amounts due under this Note have been paid in full, such noteholder shall provide the Issuer with a properly executed U.S. Internal Revenue Service (“IRS”)
Form W-8BEN, Certificate of Foreign Status of Beneficial Owner for United States Tax Withholding (or any successor form prescribed by the IRS), certifying as to such noteholder’s status for purposes of determining exemption from United States
withholding tax, information reporting and backup withholding with respect to all payments to be made to such noteholder hereunder; (iv) if an event occurs that would require a change in the exempt status of such noteholder or any of the other
information provided on the most recent IRS Form W-8BEN (or successor form) previously submitted by such noteholder to the Issuer, such noteholder will so inform the Issuer in writing (or by submitting to the Issuer a new IRS Form W-8BEN or
successor form) within 30 days after the occurrence of such event; and (v) such noteholder will not assign or otherwise transfer this Note or any of its rights hereunder except in accordance with the provisions hereof. In the case of a Holder
that is not a United States person and that, for U.S. federal income tax purposes, is treated  

  
 3 

 
as (A) a partnership (i) the representations, warranties and covenants set forth in the preceding sentence shall apply to such Holder and the Holder’s partners or members that are
the beneficial owners of this Note for U.S. federal income tax purposes and are not United States persons, and (ii) such Holder shall provide the Issuer with an IRS Form W-8IMY along with an IRS Form W-8BEN for each of such Holder’s
partners or members (or an IRS Form W-8IMY with applicable IRS W-8BEN forms for such Holder’s partners or members) or (B) a disregarded entity, the representations, warranties and covenants set forth in the preceding sentence shall apply
to such Holder’s beneficial owner. A Holder that is not a United States person and that is treated as a partnership or disregarded entity for U.S. federal income tax purposes shall, in lieu of an IRS Form W-8, provide IRS Form W-9 certifying
exemption from U.S. backup withholding with respect to any of such Holder’s partners or members that are United States persons. 
 In
order to qualify as a “registered note” for purposes of the Code, transfer of this Note may be effected only by (i) surrender of this Note to the Issuer and the re-issuance of this Note to the transferee, or the Issuer’s issuance
to the Holder of a new note in the same form as this Note but with the transferee denoted as the Holder, or (ii) the recording of the identity of the transferee by the Affiliate of the Holder that is maintaining a record ownership register of
this Note as agent to, and on behalf of, the Issuer. Such Affiliate in its capacity as such agent shall notify the Issuer in writing immediately upon any change in such identity. The terms and conditions of this Note shall be binding upon and inure
to the benefit of the Issuer and the Holder and their permitted assigns; provided, however, that if any such assignment (whether by operation of law, by way of transfer or participation, or otherwise) is to any noteholder that is not a “United
States person” within the meaning of Section 7701(a)(30) of the Code, then such noteholder shall submit to the Issuer on or before the date of such assignment an IRS Form W-8BEN (or any successor form) certifying as to such
noteholder’s status for purposes of determining exemption from United States withholding tax, information reporting and backup withholding with respect to all payments to be made to such noteholder under the new note (or other instrument). Any
attempted transfer in violation of the relevant provisions of this Note shall be void and of no force and effect. Until there has been a valid transfer of this Note and of all of the rights hereunder by the Holder in accordance with this Note, the
Issuer shall deem and treat the Holder as the absolute beneficial owner and holder of this Note and of all of the rights hereunder for all purposes (including, without limitation, for the purpose of receiving all payments to be made under this
Note). 
 It is the intention of the Issuer and the Holder that this Note is to be a registered instrument and not a bearer instrument and
the provisions of this Note are to be interpreted accordingly. This Note is intended to be registered as to both principal and interest and all payments hereunder shall be made to the named Holder or, in the event of a transfer pursuant to the Note
Purchase Agreement and this Note, to the transferee identified in the record of ownership of this Note maintained by the Holder on behalf of the Issuer. Transfer of this Note may not be effected except in accordance with the provisions hereof. 

This Note constitutes a renewal and restatement of, and replacement and substitution for, that certain Secured Convertible Note dated
as of July 2, 2010 in the original principal amount of $            executed by Issuer in favor of Holder, as Assignee of
            (the “Prior Note”). The indebtedness evidenced by the Prior Note is continuing indebtedness evidenced hereby and nothing herein shall be deemed to constitute
payment, settlement or novation of the Prior Note or to release or otherwise adversely affect any Lien securing such indebtedness. 

[Signature Page Follows] 

  
 4 

 IN WITNESS WHEREOF, an authorized representative of the Issuer has executed this Note as of the
date first written above. 
  

					
	EXELIXIS, INC.
		
	By:	 	  

		 	Name:	 	
		 	Title:	 	

 Secured Convertible Note issued to
                     

 Exhibit B 

Form of Registration Rights Agreement 

[Filed separately] 

 Exhibit C 

Form of Warrants 
 [Filed
separately] 

 Exhibit D 

Intercompany Subordination Provisions 
 Each
promissory note evidencing intercompany Indebtedness (an “Intercompany Note”) incurred by Borrower owing to any Subsidiary shall have included on its face the following subordination provision (modified as appropriate to reflect the
defined terms used in the applicable Intercompany Note): 
 (a) Anything in this Intercompany Note to the contrary notwithstanding, the
Indebtedness evidenced by this Note owed by Borrower shall be subordinate and junior in right of payment, to the extent and in the manner hereinafter set forth, to all Obligations (such Obligations and other indebtedness and obligations in
connection with any renewal, refunding, restructuring or refinancing thereof, including interest thereon accruing after the commencement of any proceedings referred to in clause (i) below, whether or not such interest is an allowed claim in
such proceeding, being hereinafter collectively referred to as “Senior Indebtedness”). 
 (i) In the event of any insolvency or
bankruptcy proceedings, and any receivership, examinership, liquidation, reorganization or other similar proceedings in connection therewith, relative to Borrower or to its creditors, as such, or to its property, and in the event of any proceedings
for voluntary liquidation, dissolution or other winding up of Borrower, whether or not involving insolvency or bankruptcy, then (x) the holders of Senior Indebtedness shall be paid in full in cash in respect of all amounts constituting Senior
Indebtedness before any holder of this Intercompany Note (a “Holder”) is entitled to receive (whether directly or indirectly), or make any demands for, any payment on account of this Intercompany Note and (y) until the holders of
Senior Indebtedness are paid in full in cash in respect of all amounts constituting Senior Indebtedness, any payment or distribution to which such Holder would otherwise be entitled (other than debt securities of the Borrower that are subordinated,
to at least the same extent as this Intercompany Note, to the payment of all Senior Indebtedness then outstanding (such securities being hereinafter referred to as “Restructured Debt Securities”)) shall be made to the holders of Senior
Indebtedness. 
 (ii) If any default occurs and is continuing with respect to any Senior Indebtedness (including any Event of Default under
the Note Purchase Agreement), then no payment or distribution of any kind or character shall be made by or on behalf of Borrower or any other Person on its behalf with respect to this Intercompany Note. 

(iii) If any payment or distribution of any character by Borrower, whether in cash, securities or other property (other than Restructured Debt
Securities), in respect of this Intercompany Note shall (despite these subordination provisions) be received by any Holder in violation of clause (i) or (ii) before all Senior Indebtedness shall have been paid in full in cash, such

 
payment or distribution shall be held in trust for the benefit of, and shall be paid over or delivered to the holders of Senior Indebtedness, to the extent necessary to pay all Senior
Indebtedness in full in cash. 
 (iv) To the fullest extent permitted by law, no present or future holder of Senior Indebtedness shall be
prejudiced in its right to enforce the subordination of this Intercompany Note by any act or failure to act on the part of Borrower or by any act or failure to act on the part of such holder or any trustee or agent for such holder. Each Holder and
Borrower hereby agree that the subordination of this Intercompany Note is for the benefit of the holders of Senior Indebtedness and the holders of Senior Indebtedness are obligees under this Intercompany Note to the same extent as if their names
were written herein as such and holders of Senior Indebtedness may proceed to enforce the subordination provisions herein. 
 (vi) Nothing
contained in this subordination provision is intended to or will impair, as between Borrower and each Holder, the obligations of Borrower, which are absolute and unconditional, to pay to such Holder the principal of and interest on this Intercompany
Note as and when due and payable in accordance with its terms, or is intended to or will affect the relative rights of such Holder and other creditors of Borrower other than the holders of Senior Indebtedness.

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00225-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00225-of-00352.parquet"}]]