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                                                                     EXHIBIT 4.1


               CERTIFICATE OF DESIGNATION, PREFERENCES AND RIGHTS
                OF SERIES A JUNIOR PARTICIPATING PREFERRED STOCK
                                       OF
                         LA JOLLA PHARMACEUTICAL COMPANY

      The undersigned, Steven B. Engle, the President of LA JOLLA PHARMACEUTICAL
COMPANY, a Delaware corporation (the "CORPORATION"), does hereby certify that:

      1. Pursuant to the authority conferred upon the Board of Directors by the
Certificate of Incorporation of the Corporation, and Section 151(g) of the
Delaware General Corporation Law, on May 21, 1999, the Board of Directors
adopted the following resolutions fixing the relative rights, preferences and
limitations of the Series A Junior Participating Preferred Stock, par value
$0.01, as follows:

            RESOLVED, that pursuant to the authority vested in the Board of
      Directors of the Corporation by the Amended and Restated Certificate of
      Incorporation, the Board of Directors hereby designates the powers,
      preferences and relative, participating, optional and other rights of the
      Corporation's Series A Junior Participating Preferred Stock, and the
      qualifications, limitations and restrictions thereof as follows:

            1. DESIGNATION AND AMOUNT. The shares of such series shall be
      designated as "SERIES A JUNIOR PARTICIPATING PREFERRED STOCK" and the
      number of shares constituting such series shall be 100,000. Such number of
      shares may be increased or decreased by resolution of the Board of
      Directors; provided, that no decrease shall reduce the number of shares of
      Series A Junior Participating Preferred Stock to a number less than the
      number of shares then outstanding plus the number of shares reserved for
      issuance upon the exercise of outstanding options, rights or warrants or
      upon the conversion of any outstanding securities issued by the
      Corporation convertible into Series A Junior Participating Preferred
      Stock.

            2. DIVIDENDS AND DISTRIBUTIONS.

            (a) Subject to the prior and superior rights of the holders of any
      shares of any series of Preferred Stock ranking prior and superior to the
      shares of Series A Junior Participating Preferred Stock with respect to
      dividends, the holders of shares of Series A Junior Participating
      Preferred Stock shall be entitled to receive, when, as and if declared by
      the Board of Directors out of funds legally available for the purpose,
      quarterly dividends payable in cash on the 15th day of January, April,
      July and October of each year (each a "QUARTERLY DIVIDEND PAYMENT DATE"),
      commencing on the first Quarterly Dividend Payment Date after the first
      issuance of a share or fraction of a share of Series A Junior
      Participating Preferred Stock, in an amount per share (rounded to the
      nearest cent) equal to the greater of

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      (a) $0.25 or (b) subject to the provision for adjustment hereinafter set
      forth, 1,000 times the aggregate per share amount of all cash dividends,
      and 1,000 times the aggregate per share amount (payable in kind) of all
      non-cash dividends or other distributions other than a dividend payable in
      shares of Common Stock or a subdivision of the outstanding shares of
      Common Stock (by reclassification or otherwise), declared on the common
      stock, par value $0.01 per share, of the Corporation (the "COMMON STOCK")
      since the immediately preceding Quarterly Dividend Payment Date, or, with
      respect to the first Quarterly Dividend Payment Date, since the first
      issuance of any share or fraction of a share of Series A Junior
      Participating Preferred Stock. In the event the Corporation shall at any
      time after November 19, 1998 (the "RIGHTS DECLARATION DATE") (i) declare
      any dividend on Common Stock payable in shares of Common Stock, (ii)
      subdivide the outstanding Common Stock or (iii) combine the outstanding
      Common Stock into a smaller number of shares, then in each such case the
      amount to which holders of shares of Series A Junior Participating
      Preferred Stock were entitled immediately prior to such event under clause
      (b) of the preceding sentence shall be adjusted by multiplying such amount
      by a fraction, the numerator of which is the number of shares of Common
      Stock outstanding immediately after such event and the denominator of
      which is the number of shares of Common Stock that were outstanding
      immediately prior to such event.

            (b) The Corporation shall declare a dividend or distribution on the
      Series A Junior Participating Preferred Stock as provided in paragraph (a)
      above as a condition to declaration of a dividend or distribution on the
      Common Stock (other than a dividend payable in shares of Common Stock);
      provided that, in the event that no dividend or distribution shall have
      been declared on the Common Stock during the period between any Quarterly
      Dividend Payment Date, a dividend of $0.25 per share on the Series A
      Junior Participating Preferred Stock shall nevertheless be payable on such
      subsequent Quarterly Dividend Payment Date.

            (c) Dividends shall begin to accrue and be cumulative on outstanding
      shares of Series A Junior Participating Preferred Stock from the Quarterly
      Dividend Payment Date next preceding the date of issue of such shares of
      Series A Junior Participating Preferred Stock, unless the date of issue of
      such shares is prior to the record date for the first Quarterly Dividend
      Payment Date, in which case dividends on such shares shall begin to accrue
      from the date of issue of such shares, or unless the date of issue is a
      Quarterly Dividend Payment Date or is a date after the record date for the
      determination of holders of shares of Series A Junior Participating
      Preferred Stock entitled to receive a quarterly dividend and before such
      Quarterly Dividend Payment Date, in either of which events such dividends
      shall begin to accrue and be cumulative from such Quarterly Dividend
      Payment Date. Accrued but unpaid dividends shall not bear interest.
      Dividends paid on the shares of Series A Junior Participating Preferred
      Stock in an amount less than the total amount of such dividends at the
      time accrued and payable on


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      such shares shall be allocated pro rata on a share-by-share basis among
      all such shares at the time outstanding. The Board of Directors may fix a
      record date for the determination of holders of shares of Series A Junior
      Participating Preferred Stock entitled to receive payment of a dividend or
      distribution declared thereon, which record date shall be no more than 30
      days prior to the date fixed for the payment thereof.

            3. VOTING RIGHTS. The holders of shares of Series A Junior
      Participating Preferred Stock shall have the following voting rights:

            (a) Subject to the provision for adjustment hereinafter set forth,
      each share of Series A Junior Participating Preferred Stock shall entitle
      the holder thereof to 1,000 votes on all matters submitted to a vote of
      the stockholders of the Corporation. In the event the Corporation shall at
      any time after the Rights Declaration Date (i) declare any dividend on
      Common Stock payable in shares of Common Stock, (ii) subdivide the
      outstanding Common Stock, or (iii) combine the outstanding Common Stock
      into a smaller number of shares, then in each case the number of votes per
      share to which holders of shares of Series A Junior Participating
      Preferred Stock were entitled immediately prior to such event shall be
      adjusted by multiplying such number by a fraction, the numerator of which
      is the number of shares of Common Stock outstanding immediately after such
      event and the denominator of which is the number of shares of Common Stock
      that were outstanding immediately prior to such event.

            (b) Except as otherwise provided herein or by law, holders of Series
      A Junior Participating Preferred Stock shall have no special voting rights
      and the holders of shares of Series A Junior Participating Preferred Stock
      and the holders of shares of Common Stock shall vote together as one class
      on all matters submitted to a vote of stockholders of the Corporation.

            4. CERTAIN RESTRICTIONS.

            (a) Whenever quarterly dividends or other dividends or distributions
      payable on the Series A Junior Participating Preferred Stock as provided
      in Section 2 are in arrears, thereafter and until all accrued and unpaid
      dividends and distributions, whether or not declared, on shares of Series
      A Junior Participating Preferred Stock outstanding shall have been paid in
      full, the Corporation shall not:

                  (i) declare or pay dividends on, make any other distribution
      on, or redeem or purchase or otherwise acquire for consideration any
      shares of stock ranking junior (either as to dividends or upon
      liquidation, dissolution or winding up) to the Series A Junior
      Participating Preferred Stock;

                  (ii) declare or pay dividends on or make any other
      distributions on any shares of stock ranking on a parity (either as to
      dividends or upon liquidation, dissolution or winding up) with the Series
      A Junior Participating


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      Preferred Stock, except dividends paid ratably on the Series A Junior
      Participating Preferred Stock and all such parity stock on which dividends
      are payable or in arrears in proportion to the total amounts to which the
      holders of all such shares are then entitled;

                  (iii) redeem or purchase or otherwise acquire for
      consideration any shares of any stock ranking junior (either as to
      dividends or upon liquidation, dissolution or winding up) to the Series A
      Junior Participating Preferred Stock, provided that the Corporation may at
      any time redeem, purchase or otherwise acquire shares of any such junior
      stock in exchange for shares of any stock of the Corporation ranking
      junior (either as to dividends or upon dissolution, liquidation or winding
      up) to the Series A Junior Participating Preferred Stock;

                  (iv) redeem or purchase or otherwise acquire for consideration
      any shares of Series A Junior Participating Preferred Stock, or any shares
      of stock ranking on a parity with the Series A Junior Participating
      Preferred Stock, except (i) in exchange for shares of any stock of the
      Corporation ranking junior (either as to dividends or upon dissolution,
      liquidation or winding up) to the Series A Junior Participating Preferred
      Stock, or (ii) in accordance with a purchase offer made in writing or by
      publication (as determined by the Board of Directors) to all holders of
      such shares upon such terms as the Board of Directors, after consideration
      of the respective annual dividend rates and other relative rights and
      preferences of the respective series and classes, shall determine in good
      faith will result in fair and equitable treatment among the respective
      series or classes.

            (b) The Corporation shall not permit any subsidiary of the
      Corporation to purchase or otherwise acquire for consideration any shares
      of stock of the Corporation unless the Corporation could, under paragraph
      (a) of this Section 4, purchase or otherwise acquire such shares at such
      time and in such manner.

            5. REACQUIRED SHARES. Any shares of Series A Junior Participating
      Preferred Stock purchased or otherwise acquired by the Corporation in any
      manner whatsoever shall be retired and canceled promptly after the
      acquisition thereof. All such shares shall upon their cancellation become
      authorized but unissued shares of Preferred Stock and may be reissued as
      Series A Junior Participating Preferred Stock or as part of a new series
      of Preferred Stock to be created by resolution or resolutions of the Board
      of Directors, subject to the conditions and restrictions on issuance set
      forth herein.

            6. LIQUIDATION, DISSOLUTION OR WINDING UP.

            (a) Upon any liquidation (voluntary or otherwise), dissolution or
      winding up of the Corporation, no distribution shall be made to the
      holders of shares of stock ranking junior (either as to dividends or upon
      liquidation, dissolution or winding up) to the Series A Junior
      Participating Preferred Stock unless, prior thereto, the holders of shares
      of Series A Junior Participating


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      Preferred Stock shall have received $1,000 per share, plus an amount equal
      to accrued and unpaid dividends and distributions thereon, whether or not
      declared, to the date of such payment (the "SERIES A LIQUIDATION
      PREFERENCE"). Following the payment of the full amount of the Series A
      Liquidation Preference, no additional distributions shall be made to the
      holders of shares of Series A Junior Participating Preferred Stock unless,
      prior thereto, the holders of shares of Common Stock shall have received
      an amount per share (the "COMMON ADJUSTMENT") equal to the quotient
      obtained by dividing (i) the Series A Liquidation Preference by (ii) 1,000
      (as appropriately adjusted as set forth in subparagraph (c) below to
      reflect such events as stock splits, stock dividends and recapitalizations
      with respect to the Common Stock) (such number in clause (ii), the
      "ADJUSTMENT NUMBER"). Following the payment of the full amount of the
      Series A Liquidation Preference and the Common Adjustment in respect of
      all outstanding shares of Series A Junior Participating Preferred Stock
      and Common Stock, respectively, holders of Series A Junior Participating
      Preferred Stock and holders of shares of Common Stock shall receive their
      ratable and proportionate share of remaining assets to be distributed in
      the ratio of the Adjustment Number to one (1) with respect to such
      Preferred Stock and Common Stock, on a per share basis, respectively.

            (b) In the event, however, that there are not sufficient assets
      available to permit payment in full of the Series A Liquidation Preference
      and the liquidation preferences of all other series of Preferred Stock, if
      any, which rank on a parity with the Series A Junior Participating
      Preferred Stock, then such remaining assets shall be distributed ratably
      to the holders of such parity shares in proportion to their respective
      liquidation preferences. In the event that there are not sufficient assets
      available to permit payment in full of the Common Adjustment, then such
      remaining assets shall be distributed ratably to the holders of Common
      Stock.

            (c) In the event the Corporation shall at any time after the Rights
      Declaration Date (i) declare any dividend on Common Stock payable in
      shares of Common Stock, (ii) subdivide the outstanding Common Stock, or
      (iii) combine the outstanding Common Stock into a smaller number of
      shares, then in each such case the Adjustment Number in effect immediately
      prior to such event shall be adjusted by multiplying such Adjustment
      Number by a fraction, the numerator of which is the number of shares of
      Common Stock outstanding immediately after such event and the denominator
      of which is the number of shares of Common Stock that were outstanding
      immediately prior to such event.

            7. CONSOLIDATION, MERGER, ETC. In case the Corporation shall enter
      into any consolidation, merger, combination or other transaction in which
      the shares of Common Stock are exchanged for or changed into other stock
      or securities, cash and/or any other property, then in any such case the
      shares of Series A Junior Participating Preferred Stock shall at the same
      time be similarly


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      exchanged or changed in an amount per share (subject to the provision for
      adjustment hereinafter set forth) equal to 1,000 times the aggregate
      amount of stock, securities, cash and/or any other property (payable in
      kind), as the case may be, into which or for which each share of Common
      Stock is changed or exchanged. In the event the Corporation shall at any
      time after the Rights Declaration Date (i) declare any dividend on Common
      Stock payable in shares of Common Stock, (ii) subdivide the outstanding
      Common Stock, or (iii) combine the outstanding Common Stock into a smaller
      number of shares, then in each such case the amount set forth in the
      preceding sentence with respect to the exchange or change of shares of
      Series A Junior Participating Preferred Stock shall be adjusted by
      multiplying such amount by a fraction, the numerator of which is the
      number of shares of Common Stock outstanding immediately after such event
      and the denominator of which is the number of shares of Common Stock that
      were outstanding immediately prior to such event.

            8. NO REDEMPTION. The shares of Series A Junior Participating
      Preferred Stock shall not be redeemable.

            9. RANKING. The Series A Junior Participating Preferred Stock shall
      rank junior to all other series of the Corporation's preferred stock, if
      any, as to the payment of dividends and the distribution of assets, unless
      the terms of any such series shall provide otherwise.

            10. AMENDMENT. If there is any Series A Junior Participating
      Preferred Stock outstanding, the Amended and Restated Certificate of
      Incorporation of the Corporation shall not be further amended in any
      manner which would materially alter or change the powers, preferences or
      special rights of the Series A Junior Participating Preferred Stock so as
      to affect them adversely without the affirmative vote of the holders of a
      majority or more of the outstanding shares of Series A Junior
      Participating Preferred Stock, voting separately as a class.

            11. FRACTIONAL SHARES. Series A Junior Participating Preferred Stock
      may be issued in fractions of a share, which shall entitle the holder, in
      proportion to such holder's fractional shares, to exercise voting rights,
      receive dividends, participate in distributions and to have the benefit of
      all other rights of holders of Series A Junior Participating Preferred
      Stock.

            RESOLVED FURTHER, that the Chief Executive Officer, the President or
      any Vice President and the Secretary or any Assistant Secretary of the
      Corporation be, and they hereby are, authorized and directed to prepare
      and file a Certificate of Designation, Preferences and Rights in
      accordance with the foregoing resolution and the provisions of Delaware
      law and to take such actions as they may deem necessary or appropriate to
      carry out the intent of the foregoing resolution."


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      IN WITNESS WHEREOF, this Certificate of Designation is executed on May 21,
1999.

                                    LA JOLLA PHARMACEUTICAL COMPANY,
                                    a Delaware corporation

                                    By:   /s/ Steven B. Engle
                                          --------------------------------------
                                          Steven B. Engle
                                          Chairman of the Board,
                                          President, and Chief
                                          Executive Officer


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