LA JOLLA PHARMACEUTICAL COMPANY SECURITIES PURCHASE AGREEMENT

EXHIBIT 10.2

EXECUTION VERSION

CONFIDENTIAL TREATMENT REQUESTED

Redacted Portions are indicated by [****]

LA JOLLA PHARMACEUTICAL COMPANY

SECURITIES PURCHASE AGREEMENT

THIS SECURITIES PURCHASE AGREEMENT (this “ Agreement ”), dated as of January 4, 2009, is executed by and between La Jolla Pharmaceutical Company, a Delaware corporation (the “ Company ”), and BioMarin Pharmaceutical Inc., a Delaware corporation (the “ Purchaser ”).

RECITALS

WHEREAS, the Purchaser and the Company are parties to a Development and Commercialization Agreement dated as the date hereof relating to the development and commercialization of Riquent ^® (the “ Collaboration Agreement ”);

WHEREAS, as partial consideration for certain obligations pursuant to the Collaboration Agreement, the Purchaser and the Company have agreed that the Company will issue and sell to the Purchaser and the Purchaser will purchase from the Company shares of the Company’s Series B-1 Convertible Preferred Stock, $0.01 par value per share, and possibly shares of the Company’s Series B-2 Convertible Preferred Stock and Series B-3 Convertible Preferred Stock, each $0.01 par value per share (the Series B-1 Convertible Preferred Stock, the Series B-2 Convertible Preferred Stock and the Series B-3 Convertible Preferred Stock being collectively referred to hereinafter as the “ Series B Convertible Preferred Stock ”), at such times or in connection with such events as are specified herein and in Sections 7.2-7.5 of the Collaboration Agreement;

WHEREAS, the shares of Series B Convertible Preferred Stock issued to the Purchaser shall have the rights, preferences and privileges and be convertible into shares of the Company’s common stock, par value $0.01 per share (the “ Common Stock ”) all as specified in each series’ applicable certificate of designation, the form of which shall be equivalent to the Certificate of Designation for the Series B-1 Convertible Preferred Stock attached hereto as Exhibit A (the “ Certificate of Designation ”); and

WHEREAS, the Company and the Purchaser are entering into this Agreement to reflect the terms and conditions with respect to the Purchaser’s purchase of shares of Series B Convertible Preferred Stock from the Company (any such shares as purchased by the Purchaser are hereinafter referred to as the “ Shares ”)).

NOW, THEREFORE, in respect of the foregoing premises and for other good and valuable consideration, the receipt and sufficiency of which are hereby acknowledged, the parties hereto agree as set forth below. Any capitalized terms that are not defined herein shall have the meaning defined for such term in the Collaboration Agreement.

AGREEMENT

SECTION 1. PURCHASE OF SHARES

1.1 Authorization of Sale . On or prior to the date of this Agreement, the Company’s Board of Directors (the “ Board ”) shall have authorized the sale and issuance of the Shares and the transactions contemplated by this Agreement, subject to the terms and conditions contained herein.

1.2 Purchase and Sale . Subject to the terms and conditions of this Agreement and the Collaboration Agreement, on the date hereof, the Company agrees to sell to the Purchaser, and the Purchaser agrees to purchase from the Company, 3,391,035 Shares (the “ Initial Investment ”) at a purchase price per share of $2.21171, in the case of the Initial Closing, or, in the case of a Subsequent Closing (as defined below) at a price per common share equivalent (based on the conversion ratio provided for in the applicable Certificate of Designation, as adjusted) equal to one hundred ten percent (110%) of the average closing price of the Common Stock of the Company as reported on the NASDAQ stock market or such other reporting service as the stock is then quoted if not then quoted on NASDAQ (and if not then traded at the value determined by an investment bank selected consistent with the provisions of Section 14.3 of the Collaboration Agreement), for the ten (10) consecutive trading days commencing five (5) trading days immediately prior to the date the Company has publicly announced the event that triggered such payment ( i.e. , the P-Value Achievement, or in the case of such payment where there is no P-Value Achievement, the Company’s first public announcement of the results of the Second Interim Efficacy Analysis or the first public announcement of the approval of an NDA for the Product under Section 7.13 of the Collaboration Agreement (the “ Announcement of Results ”)). Notwithstanding the foregoing, in no event will the price per common share equivalent for the Shares issued in a Subsequent Closing (based on the conversion ratio provided for in the applicable Certificate of Designation, as adjusted) be less than $0.73724.

1.3 Purchase and Sale of Additional Shares .

(A) The Company has granted the Purchaser the right to purchase shares of Series B-2 Convertible Preferred Stock and Series B-3 Convertible Preferred Stock pursuant to the Collaboration Agreement. If the Purchaser exercises its right to purchase such additional Shares then, subject to the terms and conditions of this Agreement, the Company agrees to sell to the Purchaser, and the Purchaser agrees to purchase from the Company, that number of Shares determined by dividing the amount of the dollar investment by the Purchaser by the purchase price per share calculated in accordance with Section 1.2 of this Agreement. Each closing relating to the purchase of Shares following the Initial Closing shall be defined herein as a “Subsequent Closing,” and the Initial Closing and the Subsequent Closings shall be defined herein as the “ Closings .”

(B) Notwithstanding anything to the contrary set forth in subsection 1.3(A), if the number of Shares agreed to be purchased by the Purchaser at any Subsequent Closing, when coupled with all other shares of Series B Convertible Preferred Stock owned by the Purchaser, would exceed the maximum number of Shares allowed by NASDAQ Marketplace Rule 4350(i)(1)(B) without the approval of a majority of the total votes cast on the proposal by the stockholders of the Company, and such stockholder approval has not yet been obtained prior to such Subsequent Closing then at the relevant Closing, the Purchaser shall only be obligated to purchase that number of Shares permissible without stockholder approval under NASDAQ Marketplace Rule 4350(i)(1)(B). The Purchaser shall thereafter be obligated to purchase any Shares originally agreed to be purchased but not so purchased at such Closing due to the provisions of the previous sentence, subject to reduction as provided for in the next sentence, as promptly as practicable following such time as stockholder approval has been obtained by the Company (but in no event later than thirty (30) days following such approval). If the Company’s stockholders do not approve all purchases of Shares in accordance with NASDAQ Marketplace Rule 4350(i)(1)(B) on or before July 1, 2009, then any pending or future obligations to purchase Shares under this Agreement in excess of the maximum number of shares allowable under NASDAQ Marketplace Rule 4350(i)(1)(B) without stockholder approval shall be terminated or disallowed and the amounts payable to the Company under Sections 7.2, 7.3, 7.4 and 7.13 of the Collaboration Agreement shall be correspondingly reduced by the amount of money the Purchaser was entitled to invest in the Company but could not due to the limitations imposed by NASDAQ Marketplace Rule 4350(i)(1)(B) without any further obligation of the Purchaser to provide such monies to the Company. By way of example, if under Section 7.3(a)(ii)(x) of the Collaboration Agreement the Purchaser receives notice of a Non-Futile Determination and the Purchaser determines to continue its participation under the Collaboration Agreement by paying to the Company $22,500,000, including $5,000,000 in the form of an equity investment, but because the Company has not yet received stockholder approval under NASDAQ Marketplace Rule 4350(i)(1)(B), the Purchaser can only purchase $3,000,000 of Shares, then the Purchaser shall purchase the $3,000,000 of Shares and the Purchaser’s obligation to purchase the additional $2,000,000 of Shares shall be deferred until such stockholder approval is obtained. Notwithstanding the foregoing, if such stockholder approval is not obtained by July 1, 2009, then the Purchaser’s obligation under Section 7.3(a)(ii)(x) of the Collaboration Agreement shall be reduced from $22,500,000 to $20,500,000 and the Purchaser shall have been deemed to satisfy in full its payment obligation to the Company under such provision and if thereafter under Section 7.4 of the Collaboration Agreement the Purchaser receives notice of a P-Value Achievement, the Purchaser’s payment obligation shall be reduced from $55,000,000 to $40,000,000 and the right to pay a portion of such amount by making an equity investment shall be extinguished.

SECTION 2. CLOSING, DELIVERY AND PAYMENT

2.1 Initial Closing . The initial closing of the sale and purchase of the Initial Investment (the “ Initial Closing ”) shall take place on January 20, 2009, at the offices of Wilson Sonsini Goodrich & Rosati, Professional Corporation, 650 Page Mill Road, Palo Alto, California 94304, or at such other time or place, if any, as the Company and the Purchaser may mutually agree. As used herein, a “ Business Day ” means any day which is not (i) a Saturday or a Sunday, or (ii) a day on which banking institutions in California are authorized or obligated by law or regulation to close, and the “ Closing Date ” shall mean the date on which the applicable Closing, takes place.

2.2 Subsequent Closings. In accordance with the Collaboration Agreement, if any Subsequent Closing occurs, the purchase and sale of that number of Shares calculated in accordance with Section 7.5 of the Collaboration Agreement shall take place at the offices of Wilson Sonsini Goodrich & Rosati, Professional Corporation, 650 Page Mill Road, Palo Alto, California 94304 within fifteen (15) Business Days (subject to the closing conditions in Section 5 being satisfied) following receipt by the Company of the written notice specified in Section 7.5 of the Collaboration Agreement, or at such other place and/or time, if any, as the Company and the Purchaser may mutually agree.

2.3 Delivery . At each Closing, subject to the terms and conditions hereof, the Company will deliver to the Purchaser a certificate representing the number of Shares to be purchased by the Purchaser, against payment of the purchase price therefor in immediately available funds by check or wire transfer to an account designated by the Company.

SECTION 3. REPRESENTATIONS AND WARRANTIES OF THE COMPANY

As a material inducement to the Purchaser to enter into and perform its obligations under this Agreement, the Company hereby represents and warrants to the Purchaser as of the date hereof, and with respect to a Subsequent Closing, as of the Closing Date thereof (except for representations and warranties that speak only as of a specific date (which shall true and correct as of such date)), as follows:

3.1 Organization and Standing . The Company is a corporation duly organized, validly existing and in good standing under the laws of the State of Delaware and has full corporate power and authority to conduct its business as currently conducted and to enter into and perform this Agreement, to issue Shares being purchased by the Purchaser at each Closing and to carry out the transactions contemplated by this Agreement. The Company is duly qualified or otherwise authorized to do business as a foreign corporation or other organization and is in good standing as such in every jurisdiction in which the failure to so qualify would (i) have a material adverse effect on the business, assets, liabilities (contingent or otherwise), operations, condition (financial or otherwise) and results of operations of the Company and the Subsidiary, taken as a whole, or (ii) prevent or adversely affect the enforceability or binding effect of this Agreement or the ability of the Company to perform its obligations under this Agreement (a “ Company Material Adverse Effect ”).

3.2 Subsidiary . As of the date hereof, the Company has one wholly-owned subsidiary, La Jolla Limited (the “ Subsidiary ”), which is incorporated in England. All of the outstanding shares of capital stock of the Subsidiary and any other subsidiary established by the Company after the date hereof are duly and validly authorized, are validly issued and are fully paid and nonassessable, have been offered, issued, sold and delivered in compliance in all material respects with applicable foreign, federal and state securities laws, and are owned by the Company free and clear of any Security Interest (as defined below).

3.3 Issuance of Shares . The issuance, sale and delivery of all Shares to be sold by the Company at each Closing (only with respect to Shares issued in such Closing) in accordance with this Agreement have been duly authorized by all necessary corporate action on the part of the Company. Each Share when issued, sold and delivered in accordance with the provisions of this Agreement will be duly and validly issued, fully paid and nonassessable, free of all liens, claims and encumbrances and will not be issued in violation of any co-sale, right of first refusal, preemptive rights or any other similar rights of stockholders. The Company has reserved from its duly authorized capital stock a number of shares of Common Stock at least equal to the amount of Common Stock issuable upon conversion of the Shares (only with respect to Shares issued in such Closing) in accordance with the terms specified in the Certificate of Designation applicable to such Shares. Additionally, as of the Initial Closing, the Company has reserved from its duly authorized capital stock 37,301,387 shares of Common Stock that may be issued upon conversion of the Shares purchased at the Initial Closing as well as Shares that may be issued at any Subsequent Closing (based upon an assumed issue price equal to the floor price established in Section 1.2).

3.4 Authority for Agreement . The Company has full corporate power and authority to execute and deliver this Agreement, to issue all Shares being purchased by the Purchaser at each Closing (only with respect to Shares issued in such Closing) and to perform its other obligations hereunder and thereunder. The execution, delivery and performance by the Company of this Agreement and the consummation of the transactions contemplated hereby have been duly authorized by all requisite corporate action by the Company and, when executed and delivered by the Company, this Agreement will be the valid and binding obligation of the Company, enforceable against the Company in accordance with its terms.

3.5 No Conflict . The execution, delivery and performance of this Agreement, the issuance of all Shares being purchased by the Purchaser at each Closing (only with respect to Shares issued in such Closing) and the consummation of the other transactions contemplated hereby by the Company including the conversion of the Shares into shares of Common Stock will not (a) conflict with or violate any provision of the Company’s Certificate of Incorporation (as currently in effect, the “ Certificate ”) or its corporate By-laws (as currently in effect, the “ By-Laws ”), or (b) conflict with, result in a breach of, constitute (with or without due notice or lapse of time or both) a default under, result in the acceleration of, create in any party the right to accelerate, terminate, modify or cancel, or require any notice, consent or waiver under, any material contract, lease, sublease, license, sublicense, franchise, permit, indenture, agreement or mortgage for borrowed money, instrument of indebtedness, Security Interest (as defined below) or other material arrangement to which the Company or the Subsidiary is a party. For purposes of this Agreement, “ Security Interest ” means any mortgage, pledge, security interest, encumbrance, charge, lien or similar right (whether arising by contract or by operation of law).

3.6 Consents . No consent, permit, approval, order or authorization of, or registration, qualification, designation, declaration or filing with, any court, arbitrational tribunal, administrative agency or commission or other governmental or regulatory authority or agency, including any Self-Regulatory Organization (including NASDAQ) (each of the foregoing is hereafter referred to as a “ Governmental Entity ”) or any other Person is required to be made or obtained by the Company or any of its subsidiaries in connection with the offer, issuance, sale and delivery of all Shares being purchased by the Purchaser in each Closing (only with respect to Shares issued at such Closing) or the other transactions to be consummated hereunder, as contemplated by this Agreement, including the conversion of the Shares into shares of Common Stock, except for any applicable waiting period under the Hart-Scott-Rodino Antitrust Improvements Act of 1976 (“ HSR Act ”), such filings as shall have been made prior to and shall be effective on and as of the Initial Closing, and with respect to a Subsequent Closing, as of the Closing Date thereof, and such filings required to be made after the Initial Closing, and with respect to a Subsequent Closing, after the Closing Date thereof, under applicable federal and state securities laws. Based in part on the representations made by the Purchaser in Section 4 of this Agreement, the offer and sale of Shares to the Purchaser will be in compliance with applicable federal and state securities laws.

3.7 No Solicitation or Advertisement . Neither the Company nor the Subsidiary nor any person acting on their behalf has engaged, in connection with the offering or sale of Shares, in any form of general solicitation or general advertising within the meaning of Rule 502(c) under the Securities Act, as defined below.

3.8 Securities Act Registration . Assuming that the representations and warranties of the Purchaser contained herein are true, it is not necessary in connection with the offer, sale and delivery of Shares, in the manner contemplated by this Agreement to register the Shares under the Securities Act of 1933, as amended (the “ Securities Act ”) or under applicable state securities or Blue Sky laws regulating the issuance or sale of securities.

3.9 Capitalization . As of the date hereof, the authorized capital stock of the Company consists of 225,000,000 shares of Common Stock and 8,000,000 shares of Preferred Stock. As of September 30, 2008, the issued and outstanding capital stock of the Company consists of 55,421,634 shares of Common Stock. The shares of issued and outstanding capital stock of the Company have been duly authorized and validly issued, are fully paid and nonassessable and have not been issued in violation of any state or federal laws, rules or regulations, or in violation of (and are not otherwise subject to) any preemptive or other similar rights. Options and warrants to purchase an aggregate of 14,061,010 shares of Common Stock were outstanding as of September 30, 2008. Except as disclosed in or contemplated by the SEC Filings, as defined below, the Company does not have outstanding any options to purchase, or any preemptive rights or other rights to subscribe for or to purchase, any securities or obligations convertible into, or any contracts or commitments to issue or sell, shares of its capital stock or any such options, rights, convertible securities or obligations other than options granted under the Company’s stock option plans.

3.10 SEC Filings . The Company is a reporting company and has filed all reports required to be filed by it under the Securities Act and the Securities Exchange Act of 1934, as amended (the “ Exchange Act ”), including pursuant to Section 13(a), 14(a) or 15(d) thereof, or the rules and regulations thereunder, for the three years preceding the date hereof (the foregoing materials and any materials incorporated therein by reference being collectively referred to herein as the “ SEC Filings ”) on a timely basis or has received a valid extension of such time of filing or waiver thereof and has filed any such SEC Filings prior to the expiration of any such extension. As of their respective dates, the SEC Filings complied in all material respects with the requirements of the Exchange Act and the Securities Act and the rules and regulations of the SEC promulgated thereunder, and none of the SEC Filings, when filed, contained any untrue statement of a material fact or omitted to state a material fact required to be stated therein or necessary in order to make the statements therein, in light of the circumstances under which they were made, not misleading. The SEC Filings, for purposes of all representations in this Section 3 as of a Subsequent Closing, shall include all filings filed by the Company with the SEC up to and including the date on which the Announcement of Results occurs.

3.11 Financial Statements . The financial statements filed with the SEC as a part of the SEC Filings present fairly, in all material respects, the financial position of the Company and its consolidated subsidiaries as of and at the dates indicated and the results of their operations and cash flows for the periods specified therein, subject, in the case of interim financial statements, to the normal year-end adjustments which are not expected to be material in amount. Such financial statements have been prepared in conformity with generally accepted accounting principles as applied in the United States and in effect as of the date of the applicable financial statements and supporting schedules, as applicable, applied on a consistent basis throughout the periods involved, except as may be expressly stated in the related notes thereto, and comply in all material respects with the Securities Act, the Exchange Act and the applicable rules and regulations of the SEC thereunder. Except as set forth in such financial statements included in the SEC Filings filed prior to the date hereof, neither the Company nor the Subsidiary has incurred any liabilities, contingent or otherwise, except those incurred in the ordinary course of business consistent with past practice, none of which ordinary course liabilities, individually or in the aggregate, would reasonably be expected to result in a Company Material Adverse Effect.

3.12 Eligibility for Form S-3 . The Company represents and warrants that on the date hereof the Company meets the requirements for the use of Form S-3 for registration of the sale by the Purchaser of all Shares being purchased by the Purchaser hereunder and the Company has filed all reports required to be filed by the Company with the SEC in a timely manner so as to obtain eligibility for the use of Form S-3.

3.13 No Change . Since the filing with the SEC of the Company’s most recently filed quarterly report on Form 10-Q or annual report on Form 10-K, or with respect to the Initial Closing, as set forth on Schedule 3.13 , (i) the Company has not incurred any material liabilities or material obligations, indirect, or contingent, or entered into any material oral or written agreement or other transaction which is not in the ordinary course of business and which could reasonably be expected to result in a Company Material Adverse Effect; (ii) the Company has not sustained any material loss or interference with its businesses or properties; (iii) the Company has not paid or declared any dividends or other distributions with respect to its capital stock; (iv) the Company and the Subsidiary are not in default in the payment of principal or interest on any outstanding debt obligations; (v) there has not been any change in the capital stock of the Company other than the sale of Shares hereunder and shares or options issued pursuant to the Company’s stock option plan or employee stock purchase plan and any options outstanding as of the date hereof, or indebtedness, liens or claims (other than in the ordinary course of business); (vi) the Company has not experienced any loss of the services of any key employee or material change in the composition or duties of the senior management of the Company or the Subsidiary; (vii) the Company has not made any material change to its methods of accounting; and (viii) neither the Company nor the Subsidiary has experienced any other event or condition of any character that, individually or in the aggregate, has had or would reasonably be expected to have a Material Adverse Effect.

3.14 No Actions . Except as disclosed in the SEC Filings, (i) there are no legal or governmental actions, suits, claims, investigations or proceedings pending or threatened to which the Company or the Subsidiary is or may be a part or of which property owned or leased by the Company or the Subsidiary is or may be the subject, or related to environmental or discrimination matters, which actions, suits or proceedings, individually or in the aggregate, might prevent or might reasonably be expected to materially and adversely affect the transactions contemplated by this Agreement; and (ii) no labor disturbance by the employees of the Company or the Subsidiary exists, or is threatened which would reasonably be expected to result in a Company Material Adverse Effect. Except as disclosed in the SEC Filings, neither the Company nor the Subsidiary is a party to or subject to the provisions of any injunction, judgment, decree or order of any court, regulatory body administrative agency or other governmental body which could reasonably be expected to result in a Company Material Adverse Effect.

3.15 Compliance . To the Company’s knowledge, except as disclosed in the SEC Filings, the Company and the Subsidiary have been and are conducting their respective businesses in compliance with all applicable laws, rules and regulations of the jurisdictions in which they are each conducting business, including, without limitation, all applicable local, state, federal and foreign drug or environmental laws and regulations, the violation of which could reasonably be expected to result in a Company Material Adverse Effect. Neither the Company nor the Subsidiary is in violation of any order of any court, arbitrator or governmental body. The Company is in compliance with the applicable requirements of the Sarbanes-Oxley Act of 2002, as amended, and the rules and regulations thereunder, except where such noncompliance would not have or reasonably be expected to result in a Company Material Adverse Effect.

3.16 Intellectual Property . Except as disclosed in the SEC Filings, (i) the Company believes it owns or possesses the necessary trademarks, trademark applications, service marks, service names, trade name rights, patents, patent rights, patent applications, copyrights, licenses, know-how, trade secrets and other intellectual property rights (the “ Intellectual Property ”) to enable it to conduct its business as it is being conducted as of the date hereof and as specifically described in the SEC Filings and to enter into and perform its obligations under the Collaboration Agreement; and (ii) the Company has no knowledge of any infringement by it of any trademark, trade name rights, patent rights, copyrights, trade secret or any other intellectual property rights of third parties, or of any claim made against the Company regarding any such an infringement, and no third party, to the Company’s knowledge, is infringing the Intellectual Property, in each case, which could reasonably be expected to result in a Company Material Adverse Effect. Except as disclosed in the SEC Filings, there are no material options, licenses or agreements relating to the Intellectual Property, nor is the Company bound by or a party to any options, licenses or agreements relating to the patents, patent applications, patent rights, inventions, know-how, trade secrets, trademarks, trademark applications, service marks, service names, trade names or copyrights or other intellectual property rights of any other Person. As of the date hereof, there is no claim, action or proceeding pending or, to the Company’s knowledge, threatened, that challenges the right of the Company with respect to any Intellectual Property.

3.17 Listed Securities . As of the date hereof, the Common Stock of the Company is quoted on the Nasdaq Global Market and the Company has not received any written notice with respect to the delisting of its Common Stock from NASDAQ. The Company will continue to use commercially reasonable efforts to comply with all quantitative and qualitative requirements of the NASDAQ Marketplace Rules to the extent such compliance is within the control of the Company.

3.18 No Integrated Offering . Neither the Company nor any Person acting on its behalf has, directly or indirectly, made any offers or sales of any Company security or solicited any offers to buy any security, under circumstances that would adversely affect reliance by the Company on Regulation D or Section 4(2) of the Securities Act for the exemption from registration for the transactions contemplated hereby or would require registration of any Shares under the Securities Act or would be integrated under the NASDAQ Marketplace Rules.

3.19 Investment Company . The Company is not an “investment company” or an “affiliated person” of, or “promoter” or “principal underwriter” for an investment company, within the meaning of the Investment Company Act of 1940, as amended.

3.20 Full Disclosure. All representations and warranties of the Company and all statements, schedules or certificates furnished by or on behalf of the Company to the Purchaser or its agents pursuant to this Agreement, the Collaboration Agreement or in connection with the transactions contemplated hereby and thereby, are true and correct in all material respects and do not contain any untrue statement of a material fact or omit to state a material fact required to be stated therein or necessary in order to make the statements contained therein, in light of the circumstances under which they were made, not misleading.

3.21 Waiver with Respect to Rights Plan . The Company has waived the application of that certain Rights Agreement dated as of December 2, 2008 by and between the Company and American Stock Transfer & Trust Company, LLC (the “ Rights Plan ”) to any acquisition by the Purchaser of securities of the Company pursuant to this Agreement in any Closing.

SECTION 4. REPRESENTATIONS AND WARRANTIES OF THE PURCHASER

The Purchaser hereby represents and warrants to the Company as follows:

4.1 Investment . The Purchaser is acquiring Shares for its own account, for investme