EX-4.1






AMENDMENT NO. 1 TO




AMENDED AND RESTATED RIGHTS AGREEMENT




This Amendment No. 1, effective as of January 20, 2009 (the “Amendment”), amends the
Amended and Restated Rights Agreement, dated December 2, 2008 (the “Rights Agreement”), by
and between La Jolla Pharmaceutical Company, a Delaware corporation (the “Corporation”) and
American Stock Transfer & Trust Company, LLC, a New York limited liability trust company (the
“Rights Agent”). Capitalized terms used herein but not defined herein shall have their
defined meanings set forth in the Rights Agreement.



WHEREAS, on January 4, 2009, the Corporation entered into a Securities Purchase Agreement (the
“Securities Purchase Agreement”) with BioMarin Pharmaceutical, Inc., a Delaware corporation
(“BioMarin”);



WHEREAS, pursuant to the Securities Purchase Agreement, the Corporation is issuing on the date
herewith 339,104 shares of Series B-1 Convertible Preferred Stock, par value $0.01 and may, as
contemplated in the Securities Purchase Agreement, issue to BioMarin up to 226,068 shares of Series
B-2 Convertible Preferred Stock, par value $0.01 and 678,205 shares of Series B-3 Convertible
Preferred Stock, par value $0.01 (the Series B-1, B-2 and B-3 Convertible Preferred Stock being
collectively referred to as the “Series B Preferred Stock”);



WHEREAS, BioMarin has certain preemptive rights under the Securities Purchase Agreement to
purchase Common Stock of the Company and other securities or rights convertible into, or entitling
the holder to receive directly or indirectly, additional shares of Common Stock (the
“Preemptive Shares”); and



WHEREAS, the Corporation and the Rights Agent are entering into this Amendment to permit
BioMarin to acquire the Series B Preferred Stock, any securities issued to BioMarin as a dividend
on the Series B Preferred Stock, the Common Stock issuable upon conversion of the Series B
Preferred Stock and any Preemptive Shares that may be issued to BioMarin as contemplated under the
Securities Purchase Agreement (collectively, the “Partnership Shares”) without thereby
making BioMarin an Acquiring Person or resulting in a Distribution Date.



NOW, THEREFORE, the parties hereby agree as follows:




	 	1.	 	Section 1(a) is hereby deleted in its entirety and the following is inserted in
lieu thereof:





“(a) “Acquiring Person” shall mean any Person (as such term
is hereinafter defined) who or which, together with all Affiliates
(as such term is hereinafter defined) and Associates (as such term
is hereinafter defined) of such Person, shall be the Beneficial
Owner (as such term is hereinafter defined) of 15% or more of the
            shares of Common Stock of the Company then outstanding, but shall
not include (i) the Company, (ii) any Subsidiary (as such term is
hereinafter defined) of the Company, (iii) any employee benefit plan
or compensation arrangement of the Company or any Subsidiary of the
Company or (iv) any Person holding shares of Common Stock of the
Company organized, appointed or established by the Company or any
Subsidiary of the Company for or pursuant to the terms of any such
employee benefit plan or compensation arrangement (the Persons
described in clauses (i) through (iv) above are referred to herein
as “Exempt Persons”); provided, however,
that the term “Acquiring Person” shall not include: (A) BioMarin
Pharmaceutical Inc. and its Affiliates and Associates (collectively,
“BioMarin”), to the extent BioMarin becomes the Beneficial
Owner of 15% or more of the shares of Common Stock of the Company
then outstanding solely due to BioMarin’s Beneficial Ownership of
the Partnership Shares; or (B) any Grandfathered Person, unless such
Grandfathered Person becomes the Beneficial Owner of a percentage of
the shares of Common Stock of the Company then outstanding equal to
or exceeding such Grandfathered Person’s Grandfathered Percentage.
For the avoidance of doubt, if BioMarin becomes or is the Beneficial
Owner of 15% or more of the shares of Common Stock of the Company
then outstanding (including the Partnership Shares) and at such time
BioMarin is deemed to be the Beneficial Owner of any shares of
Common Stock of the Company other than the Partnership Shares, then
BioMarin shall be deemed an Acquiring Person hereunder.



Notwithstanding the foregoing, no Person shall become an “Acquiring
Person” as the result of an acquisition by the Company of Common
Stock of the Company which, by reducing the number of shares
outstanding, increases the proportionate number of shares
Beneficially Owned by such Person to 15% or more (or, in the case of
a Grandfathered Person, the Grandfathered Percentage applicable to
such Grandfathered Person) of the shares of Common Stock of the
Company then outstanding; provided, however, that if
a Person shall become the Beneficial Owner of 15% or more (or, in
the case of a Grandfathered Person, the Grandfathered Percentage
applicable to such Grandfathered Person) of the shares of Common
Stock of the Company then outstanding by reason of share purchases
by the Company and shall, after such share purchases by the Company,
become the Beneficial Owner of any additional shares (other than
pursuant to a stock split, stock dividend or similar transaction) of
Common Stock of the Company and immediately thereafter be the
Beneficial Owner of 15% or more (or, in the case of a Grandfathered
Person, the Grandfathered Percentage applicable to such
Grandfathered Person) of the shares of Common Stock of the Company
then outstanding, then such Person shall be deemed to be an
“Acquiring Person.” In addition, notwithstanding the foregoing, and
notwithstanding anything to the contrary provided in the Agreement
including without limitation in Sections 1(jj), 3(a) or 27, a Person
shall not be an “Acquiring Person” if the Board of Directors of the
Company determines at any time that a Person who would otherwise be
an “Acquiring Person,” has become such without intending to become
an “Acquiring Person,” and such Person divests as promptly as
practicable (or within such period of time as the Board of Directors
of the Company determines is reasonable) a sufficient number of
            shares of Common Stock of the Company (or, for the avoidance of
doubt, with respect to any Derivative Common Shares, terminates the
subject derivative transaction or transactions or disposes of the
subject derivative security or securities) so that such Person would
no longer be an “Acquiring Person,” as defined pursuant to the
foregoing provisions of this Section 1(a).”




	 	2.	 	Section 3(a) is hereby deleted in its entirety and the following is inserted in
lieu thereof:





“From the date hereof until the earlier of (i) the Close of Business
on the tenth calendar day after the Stock Acquisition Date or
(ii) the Close of Business on the tenth Business Day (or such later
calendar day, if any, as the Board of Directors of the Company may
determine in its sole discretion) after the date a tender or
exchange offer by any Person, other than an Exempt Person, is first
published or sent or given within the meaning of Rule 14d-4(a) of
the Exchange Act, or any successor rule, if, upon consummation
thereof, such Person could become, or would be, the Beneficial Owner
of 15% or more (or, in the case of a Grandfathered Person, the
Grandfathered Percentage applicable to such Grandfathered Person) of
the shares of Common Stock of the Company then outstanding
(including any such date which is after the date of this Agreement
and prior to the issuance of the Rights) (the earliest of such dates
being herein referred to as the “Distribution Date”),
(x) the Rights will be evidenced (subject to the provisions of
Section 3(b) hereof) by the certificates for the Common Stock of the
Company registered in the names of the holders of the Common Stock
of the Company (which certificates for Common Stock of the Company
shall be deemed also to be certificates for Rights) and not by
separate certificates, and (y) the Rights will be transferable only
in connection with the transfer of the underlying shares of Common
Stock of the Company. As soon as practicable after the Distribution
Date, the Rights Agent will, at the Company’s expense send, by
first-class, insured, postage prepaid mail, to each record holder of
the Common Stock of the Company as of the Close of Business on the
Distribution Date, at the address of such holder shown on the
records of the Company, one or more certificates, in substantially
the form of Exhibit B hereto (the “Right
Certificates”), evidencing one Right for each share of Common
Stock of the Company so held, subject to adjustment as provided
herein. In the event that an adjustment in the number of Rights per
share of Common Stock of the Company has been made pursuant to
Section 11(o) hereof, the Company may make the necessary and
appropriate rounding adjustments (in accordance with Section 14(a)
hereof) at the time of distribution of the Right Certificates, so
that Right Certificates representing only whole numbers of Rights
are distributed and cash is paid in lieu of any fractional Rights.
As of and after the Close of Business on the Distribution Date, the
Rights will be evidenced solely by such Right Certificates.”



3.  Except as expressly set forth in this Amendment all other terms of the Rights Agreement
shall remain in full force and effect.



4.  This Amendment shall be governed by and construed in accordance with the laws of the State
of Delaware applicable to contracts made and to be performed entirely within such State, without
regard to conflict-of-law principles.



5.  This Amendment may be executed in any number of counterparts and each of such counterparts
shall for all purposes be deemed to be an original, and all such counterparts shall together
constitute but one and the same instrument.



[The remainder of this page has been intentionally left blank; signature page follows.]







1






     IN WITNESS WHEREOF, the Corporation and the Rights Agent have executed this Amendment
effective as of the date first above written.



	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	 
	 	THE CORPORATION:

La Jolla Pharmaceutical Company,
a Delaware corporation
 	 	 
	 
	 	By:  	 	 /s/ Deirdre Gillespie	 	 
	 
	 	 	 	 	 	 
	 
	 	 	 	Deirdre Y. Gillespie, M.D. 	 	 
	 
	 	 	 	President and Chief Executive Officer 	 	 
	 

	 	 	 	 	 	 	 	 	 
	 	 	RIGHTS AGENT:
American Stock Transfer & Trust Company, LLC, a New York limited liability
company
 	 	 
	 	 	By:  	 	/s/ Herbert J. Lemmer	 	 
	 	 	 	 	 	 	 
	 	 	 	 	Name:  	 	Herbert J. Lemmer	 	 
	 	 	 	 	Title:  	 	Vice President	 	 
	 








2