XENOGEN CORP
S-1/A, EX-3.1(I), 2000-12-29
COMMERCIAL PHYSICAL & BIOLOGICAL RESEARCH
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                                                                  Exhibit 3.1(i)

               AMENDED AND RESTATED CERTIFICATE OF INCORPORATION

                                      OF

                              XENOGEN CORPORATION


     XENOGEN CORPORATION, a corporation organized and existing under the laws of
the State of Delaware, hereby certifies as follows:

     FIRST:  The name of this corporation is Xenogen Corporation.

     SECOND:  The original Certificate of Incorporation of the corporation was
filed with the Secretary of State of the State of Delaware on September 6, 2000
and the original name of the corporation was Xenogen Corporation.  A Certificate
of Merger whereby Xenogen Corporation, a California corporation, was merged with
and into this corporation under the name of Xenogen Corporation, a Delaware
corporation, was filed with the Secretary of State of the State of Delaware on
September 11, 2000.

     THIRD: The Amended and Restated Certificate of Incorporation of said
corporation shall be amended and restated to read in full as follows:

                                   ARTICLE I

     The name of this Corporation is Xenogen Corporation (the "Corporation").

                                  ARTICLE II

     The address of the Corporation's registered office in the State of Delaware
is Corporation Trust Center, 1209 Orange Street, in the City of Wilmington,
County of New Castle, Zip code 19801.  The name of its registered agent at such
address is The Corporation Trust Company.


                                  ARTICLE III

     The purpose of this Corporation is to engage in any lawful act or activity
for which a corporation may be organized under the General Corporation Law of
Delaware.

                                  ARTICLE IV

     This Corporation is authorized to issue two classes of stock, to be
designated, respectively, "Common Stock" and "Preferred Stock."  The total
number of shares which this Corporation is authorized to issue is 63,846,501
shares, of which 40,000,000 shares are Common Stock, with a par value of $0.001,
and 23,846,501 shares are Preferred Stock, with a par value of $0.001.  Of the
Preferred Stock, 60,606 shares are designated Series A Preferred Stock, 200,000
shares are designated Series B Preferred Stock, 5,156,924 shares are designated
Series C Preferred Stock, 6,678,791 shares are designated Series D Preferred
Stock, 8,250,000 shares are designated Series E Preferred Stock and 3,500,000
shares are designated Series F Preferred Stock.
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                                   ARTICLE V

     The rights, preferences, privileges and restrictions granted to or imposed
upon the Common Stock, the Series A Preferred Stock, the Series B Preferred
Stock, the Series C Preferred Stock, the Series D Preferred Stock, the Series E
Preferred Stock and the Series F Preferred Stock are as follows:

          A.   Dividends.
               ---------

               1.   Preference Dividends.  The holders of Series A Preferred
                    --------------------
Stock, Series B Preferred Stock, Series C Preferred Stock, Series D Preferred
Stock, Series E Preferred Stock and Series F Preferred Stock shall be entitled
to receive, on a pari passu basis, dividends, out of any assets legally
                 ---- -----
available therefor, prior and in preference to any declaration or payment of any
dividend (payable other than in Common Stock or other securities and rights
convertible into or entitling the holder thereof to receive, directly or
indirectly, additional shares of Common Stock of this Corporation) on the Common
Stock of this Corporation, at the rate of $0.0264, $0.04, $0.104, $0.132, $0.34
and $10.00 per share, respectively, per annum when, as and if declared by the
board of directors.

               2.   Dividends Noncumulative.  The right to dividends on shares
                    -----------------------
of the Common Stock and Preferred Stock shall not be cumulative, and no right
shall accrue to holders of Common Stock or Preferred Stock by reason of the fact
that dividends on said shares are not declared in any prior period.

               3.   So long as any shares of Preferred Stock shall be
outstanding, no dividend, whether in cash or property, shall be paid or
declared, nor shall any other distribution be made, on any other stock of the
Corporation ("Junior Stock"), nor shall any shares of Junior Stock be purchased,
redeemed, or otherwise acquired for value by the Corporation (except for
acquisitions of Common Stock by the Corporation pursuant to agreements which
permit the Corporation to repurchase shares upon termination of services to the
Corporation or in exercise of the Corporation's right of first refusal upon a
proposed transfer) until all dividends (set for in Section A.1) on the Preferred
Stock shall have been paid or declared and set apart. In the event dividends are
paid on any share of Common Stock, an additional dividend shall be paid with
respect to all outstanding shares of Preferred Stock in an amount equal per
share (on an as-if-converted to Common Stock basis) to the amount paid or set
aside for each share of Common Stock. The provisions of this Section A.3 shall
not, however, apply to (i) a dividend payable in Common Stock, (ii) the
acquisition of shares of any Junior Stock in exchange for shares of any other
Junior Stock, or (iii) the repurchase of any outstanding securities of the
Corporation that is unanimously approved by the Corporation's Board of
Directors.

          B.   Liquidation Preference.
               ----------------------

               1.   Preference.  In the event of any liquidation, dissolution
                    ----------
or winding up of the Corporation, either voluntarily or involuntarily (a
"Liquidation"), distributions to the

                                      -2-
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shareholders of the Corporation shall be made as follows:

                    (a)  Preferred Stock Preference.  The holders of Series A
                         --------------------------
Preferred Stock, Series B Preferred Stock, Series C Preferred Stock, Series D
Preferred Stock, Series E Preferred Stock and Series F Preferred Stock shall be
entitled to receive, on a pari passu basis and prior and in preference to any
                          ---- -----
distribution of any of the assets or surplus funds of the Corporation to the
holders of Common Stock of the Corporation, an amount equal to $0.33, $0.50,
$1.30, $1.65, $4.25 and $10.00 per share of the Series A Preferred Stock, Series
B Preferred Stock, Series C Preferred Stock, Series D Preferred Stock, Series E
Preferred Stock and Series F Preferred Stock, respectively (as adjusted for any
stock dividends, combinations, splits, recapitalizations and the like with
respect to such shares), plus a further amount equal to any dividends declared
but unpaid on such shares (respectively, the "Series A Preference," the "Series
B Preference," the "Series C Preference," the "Series D Preference," the "Series
E Preference" and the "Series F Preference"). If upon such Liquidation the
assets of the Corporation are insufficient to provide for cash payment in full
described in this Section B.1(a) to the holders of Preferred Stock, the entire
assets of the Corporation as available shall be distributed pro rata among the
holders of Preferred Stock in proportion to the full preferential amount each
such holder would otherwise entitled to receive pursuant to this Section
B.1.(a).

                    (b)  Remaining Assets.  After the payment or setting apart
                         ----------------
of payment to of the Series A Preference, the Series B Preference, the Series C
Preference, the Series D Preference, the Series E Preference and the Series F
Preference, the holders of Common Stock shall be entitled to receive pro rata
the remaining assets of the Corporation in proportion to the number of shares of
Common Stock then held by them.

                    (c)  Superceding Payment.  Notwithstanding anything to the
                         -------------------
contrary in Section B.1(b), if the amount that the Series A Preferred Stock,
Series B Preferred Stock, Series C Preferred Stock, Series D Preferred Stock,
Series E Preferred Stock or Series F Preferred Stock would receive in a
Liquidation (assuming conversion of all shares of Preferred Stock to Common
Stock issuable upon conversion thereof immediately prior to the Liquidation)
(the "Converted Liquidation Amount") exceeds the Series A Preference, the Series
B Preference, Series C Preference, Series D Preference, Series E Preference or
Series F Preference (each a "Threshold Amount"), then the holder of the
applicable series shall be entitled to such higher Converted Liquidation Amount
in lieu of the applicable Threshold Amount.

               2.   Consolidation or Merger. A sale of all or substantially all
                    -----------------------
of the assets of the Corporation or a consolidation or merger of the Corporation
with or into any other Corporation or Corporations, in which the shareholders of
the Corporation immediately prior to such event do not own more than 50% of the
voting power of the surviving Corporation or its parent shall be deemed to be a
Liquidation within the meaning of this Section B, excluding any merger effected
exclusively to change the Corporation domicile (an "Acquisition"). Any
securities to be delivered to the holders of the Preferred Stock and Common
Stock upon a merger, reorganization or sale of substantially all of the assets
of the Corporation shall be valued as follows:

                    (a)  Securities not subject to investment letter or other
similar restrictions on free marketability:

                                      -3-
<PAGE>

                         (i)    If traded on a securities exchange or the Nasdaq
Stock Market, the value shall be deemed to be the average of the closing prices
of the securities on such exchange over the 30-day period ending three (3) days
prior to the closing of the transaction;

                         (ii)   If actively traded over-the-counter, the value
shall be deemed to be the average of the closing bid prices over the 30-day
period ending three (3) days prior to the closing of the transaction; and

                         (iii)  If there is no active public market, the value
shall be the fair market value thereof, as determined in good faith by the board
of directors of this Corporation.

                    (b)  The method of valuation of securities subject to
investment letter or other restrictions on free marketability shall be to make
an appropriate discount from the market value determined as above in Section
B.2.(a)(i)(ii) or (iii) to reflect the approximate fair market value thereof, as
determined in good faith by the board of directors of this Corporation.

               3.   In the event the requirements of Section B.2. are not
complied with, the Corporation shall forthwith either:

                    (a)  cause such closing to be postponed until such time as
the requirements of this Section B.2. have been complied with, or

                    (b)  cancel such transaction, in which event the rights,
preferences, privileges and restrictions of the holders of the Preferred Stock
shall revert to and be the same as such rights, preferences, privileges and
restrictions existing immediately prior to the date of the first notice referred
to in Section B.4. hereof.

               4.   The Corporation shall give each holder of record of
Preferred Stock written notice of such a Section B.2. transaction not later than
twenty (20) days prior to the shareholders' meeting called to approve such
transaction, or twenty (20) days prior to the closing of such transaction,
whichever is earlier, and shall also notify such holders in writing of the final
approval of such transaction. The first of such notices shall describe the
material terms and conditions of the impending transaction and the provisions of
Section B.2., and the Corporation shall thereafter give such holders prompt
notice of any material changes. The transaction shall in no event take place
sooner than twenty (20) days after the Corporation has given notice of any
material changes provided for herein; provided, however, that such periods may
                                      --------  -------
be shortened upon the written consent of the holders of a majority of the shares
of Preferred Stock then outstanding.

          C.   Conversion.  The holders of the Preferred Stock shall have
               ----------
conversion rights as follows (the "Conversion Rights"):

               1.   Right to Convert.  Each share of Preferred Stock shall be
                    ----------------
convertible, at the option of the holder thereof, at any time after the date of
issuance of such share at the office of the Corporation or any transfer agent
for the Preferred Stock. Each share of the Series A Preferred Stock, Series B
Preferred Stock, Series C Preferred Stock, Series D Preferred Stock, Series E
Preferred Stock and Series F Preferred Stock shall be convertible into the
number of fully paid and

                                      -4-
<PAGE>

nonassessable shares of Common Stock which results from dividing the Conversion
Price (as hereinafter defined) per share in effect for each series of Preferred
Stock at the time of conversion into the per share Conversion Value (as
hereinafter defined) of such series. The initial Conversion Price per share of
Series A Preferred Stock shall be $0.33 and the per share Conversion Value of
Series A Preferred Stock shall be $0.33; the initial Conversion Price per share
of Series B Preferred Stock shall be $0.50 and the per share Conversion Value of
Series B Preferred Stock shall be $0.50; the initial Conversion Price per share
of Series C Preferred Stock shall be $1.30 and the per share Conversion Value of
Series C Preferred Stock shall be $1.30; the initial Conversion Price per share
of Series D Preferred Stock shall be $1.65 and the per share Conversion Value of
Series D Preferred Stock shall be $1.65; the initial Conversion Price per share
of Series E Preferred Stock shall be $4.25 and the per share Conversion Value of
Series E Preferred Stock shall be $4.25; and the initial Conversion Price per
share of Series F Preferred Stock shall be $10.00 and the per share Conversion
Value of Series F Preferred Stock shall be $10.00. The Conversion Price of each
series shall be subject to adjustment from time to time as provided below. The
number of shares of Common Stock into which a series of Preferred Stock is
convertible is hereinafter referred to as the "Conversion Rate" of such series.

               2.   Automatic Conversion.  Each share of Preferred Stock shall
                    --------------------
automatically be converted into shares of Common Stock at its then effective
Conversion Rate immediately upon:

                    (a)  the closing of a firm commitment underwritten public
offering pursuant to an effective registration statement under the Securities
Act of 1933, as amended, the aggregate gross proceeds to the Corporation of
which exceed $15,000,000 and the per share price to the public of which is at
least $8.00 (subject to equitable adjustment in the event of any stock split,
stock dividend, combination, reclassification of shares or other similar event),
prior to deduction of underwriting commissions and offering expenses, or

                    (b)  the election of the holders of a majority of the shares
of Preferred Stock then outstanding.

               3.   Mechanics of Conversion.  Before any holder of Preferred
                    -----------------------
Stock shall be entitled to convert the same into shares of Common Stock, such
holder shall surrender the certificate or certificates therefor, duly endorsed,
at the office of the Corporation or of any transfer agent for the Preferred
Stock and shall give written notice to the Corporation at such office that he
elects to convert the same (except that no such written notice of election to
convert and no surrender of the stock certificate or certificates shall be
necessary in the event of an automatic conversion pursuant to paragraph C.2.
hereof). The Corporation shall, as soon as practicable thereafter, but in no
event later than ten (unless any of the Corporation's capital stock is publicly
traded in which in no event than three) business days after receipt of the
certificates representing the Preferred Stock surrendered for conversion, issue
and deliver at such office to such holder of Preferred Stock a certificate or
certificates for the number of shares of Common Stock to which such holder shall
be entitled. Such conversion shall be deemed to have been made immediately
before the close of business on the date of such surrender of the shares of
Preferred Stock to be converted, (except that in the case of an automatic
conversion pursuant to paragraph C.2. such conversion shall be deemed to have
been made either immediately before the closing of the offering referred to in
paragraph C.2.(a) or immediately upon the election of the holders of a majority
of Preferred Stock referred to in

                                      -5-
<PAGE>

paragraph C.2.(b)) and the person or persons entitled to receive the shares of
Common Stock issuable upon such conversion shall be treated for all purposes as
the record holder or holders of such shares of Common Stock at such time.

               4.   Fractional Shares.  In lieu of any fractional shares of
                    -----------------
Common Stock to which any holder of Preferred Stock would otherwise be entitled,
the Corporation shall pay cash equal to such fraction multiplied by the fair
market value of one share of Common Stock. The "fair market value" of the Common
Stock shall be determined by the following methods: (i) if the Common Stock is
traded on a securities exchange or the Nasdaq Stock Market, the "fair market
value" shall be deemed to be the closing price of the Common Stock on the
trading day prior to conversion of the Preferred Stock; (ii) if the Common Stock
is actively traded over-the-counter, the "fair market value" shall be deemed to
be the closing bid price of the Common Stock on the trading prior to conversion
of the Preferred Stock; and (iii) if there is no active public market for the
Common Stock, the "fair market value" shall be determined in good faith by the
board of directors of this Corporation. Whether or not fractional shares are
issuable upon such conversion shall be determined on the basis of the total
number of shares of Preferred Stock of each holder at the time converting into
Common Stock and the number of shares of Common Stock issuable upon such
aggregate conversion.

               5.   Adjustment of Conversion Price.  The Conversion Price of
                    ------------------------------
each series of Preferred Stock shall be subject to adjustment from time to time
as follows:

                    (a)  If the Corporation shall issue any Common Stock other
than "Excluded Stock," as defined below, for a consideration per share less than
the applicable Conversion Price in effect immediately prior to the issuance of
such Common Stock (excluding stock dividends, subdivisions, split-ups,
combinations, dividends or recapitalizations which are covered by Section
C.5.(c),(d),(e) and (f)), the applicable Conversion Price in effect immediately
after each such issuance shall forthwith (except as provided in this Section
C.5.) be adjusted to a price equal to the quotient obtained by dividing:

                         (1)  an amount equal to the sum of

                              (x)  the total number of shares of Common Stock
outstanding (including any shares of Common Stock issuable upon conversion of
the Preferred Stock) immediately prior to such issuance multiplied by the
applicable Conversion Price in effect immediately prior to such issuance, plus

                              (y)  the consideration received by the Corporation
upon such issuance, by

                         (2)  the total number of shares of Common Stock
outstanding (including any shares of Common Stock issuable upon conversion of
the Preferred Stock) immediately prior to such issuance plus the additional
shares of Common Stock issued in such issuance (but not including any additional
shares of Common Stock deemed to be issued as a result of any adjustment in the
applicable Conversion Price resulting from such issuance).

                                      -6-
<PAGE>

                              For purposes of any adjustment of a Conversion
Price pursuant to this clause (a), the following provisions shall be applicable:

                              (ii)   In the case of the issuance of Common Stock
for cash, the consideration shall be deemed to be the amount of cash paid
therefor after deducting any discounts or commissions paid or incurred by the
Corporation in connection with the issuance and sale thereof but without
deduction of any expenses payable by the Corporation.

                              (iii)  In the case of the issuance of Common Stock
for a consideration in whole or in part other than cash, the consideration other
than cash shall be deemed to be the fair market value thereof as determined by
the board of directors of the Corporation, in accordance with generally accepted
accounting treatment; provided, however, that if, at the time of such
                      --------  -------
determination, the Corporation's Common Stock is traded in the over-the-counter
market or on a national or regional securities exchange, such fair market value
as determined by the board of directors of the Corporation shall not exceed the
aggregate "Current Market Price" (as defined below) of the shares of Common
Stock being issued.

                              (iv)   In the case of issuance of (1) options to
purchase or rights to subscribe for Common Stock (other than Excluded Stock),
(2) securities by their terms convertible into or exchangeable for Common Stock
(other than Excluded Stock), or (3) options to purchase or rights to subscribe
for such convertible or exchangeable securities:

                                     (A)  the aggregate maximum number of shares
of Common Stock deliverable upon exercise of such options to purchase or rights
to subscribe for Common Stock shall be deemed to have been issued at the time
such options or rights were issued and for a consideration equal to the
consideration (determined in the manner provided in subdivisions (i) and (ii)
above), if any, received by the Corporation upon the issuance of such options or
rights plus the minimum purchase price provided in such options or rights for
the Common Stock covered thereby;

                                     (B)  the aggregate maximum number of shares
of Common Stock deliverable upon conversion of or in exchange for any such
convertible or exchangeable securities or upon the exercise of options to
purchase or rights to subscribe for such convertible or exchangeable securities
and subsequent conversion or exchange thereof, shall be deemed to have been
issued at the time such securities were issued or such options or rights were
issued and for a consideration equal to the consideration received by the
Corporation for any such securities and related options or rights (excluding any
cash received on account of accrued interest or accrued dividends), plus the
minimum additional consideration, if any, to be received by the Corporation upon
the conversion or exchange of such securities or the exercise of any related
options or rights (the consideration in each case to be determined in the manner
provided in subdivisions (i) and (ii) above);

                                     (C)  on any change in the number of shares
of Common Stock deliverable upon exercise of any such options or rights or
conversion of or exchange for such convertible or exchangeable securities, or on
any change in the minimum purchase price of such options, rights or securities,
other than a change resulting from the antidilution provisions of

                                      -7-
<PAGE>

such options, rights or securities, the Conversion Price shall forthwith be
readjusted to such Conversion Price as would have obtained had the adjustment
made upon (x) the issuance of such options, rights or securities not exercised,
converted or exchanged prior to such change, as the case may be, been made upon
the basis of such change or (y) the options or rights related to such securities
not converted or exchanged prior to such change, as the case may be, been made
upon the basis of such change; and

                                     (D)  on the expiration of any such options
or rights, the termination of any such rights to convert or exchange or the
expiration of any options or rights related to such convertible or exchangeable
securities, the Conversion Price shall forthwith be readjusted to such
Conversion Price as would have obtained had the adjustment made upon the
issuance of such options, rights, convertible or exchangeable securities or
options or rights related to such convertible or exchangeable securities, as the
case may be, been made upon the basis of the issuance of only the number of
shares of Common Stock actually issued upon the exercise of such options or
rights, upon the conversion or exchange of such convertible or exchangeable
securities or upon the exercise of the options or rights related to such
convertible or exchangeable securities, as the case may be.

                    (b)  "Excluded Stock" shall mean:

                         (i)    all shares of Common Stock issued and
outstanding on the date of the first issuance of any shares of Series F
Preferred Stock and all shares of capital stock issuable upon exercise of
options or warrants outstanding on the date of the first issuance of any shares
of Series F Preferred Stock;

                         (ii)   all shares of Common Stock into which the shares
of Preferred Stock are convertible;

                         (iii)  shares of Common Stock, warrants or options to
purchase Common Stock or other securities issued to employees, officers,
directors, scientific advisors and consultants of the Corporation pursuant to
any plan or arrangement approved by the board of directors of the Corporation;

                         (iv)   all securities issuable to lending or leasing
institutions in an aggregate not to exceed 100,000 shares pursuant to any plan
or arrangement approved by the board of directors of the Corporation including
approval by all of the Preferred Directors (as defined below); and

                         (v)    all securities issued or issuable to licensors
or corporate partners of the Corporation upon the unanimous approval of the
board of directors of the Corporation.

                    (c)  If the number of shares of Common Stock outstanding at
any time after the date hereof is increased by a stock dividend payable in
shares of Common Stock or by a subdivision or split-up of shares of Common
Stock, then, on the date such payment is made or such change is effective, the
Conversion Price of each series of Preferred Stock shall be appropriately

                                      -8-
<PAGE>

decreased so that the number of shares of Common Stock issuable on conversion of
any shares of each series of Preferred Stock shall be increased in proportion to
such increase of outstanding shares.

                    (d)  If the number of shares of Common Stock outstanding at
any time after the date hereof is decreased by a combination of the outstanding
shares of Common Stock, then, on the effective date of such combination, the
Conversion Price of each series of Preferred Stock shall be appropriately
increased so that the number of shares of Common Stock issuable on conversion of
any shares of each series of Preferred Stock shall be decreased in proportion to
such decrease in outstanding shares.

                    (e)  In case the Corporation shall declare a cash dividend
upon its Common Stock payable otherwise than out of retained earnings or shall
distribute to holders of its Common Stock shares of this capital stock (other
than Common Stock), stock or other securities of other persons, evidences of
indebtedness issued by the Corporation or other persons, assets (excluding cash
dividends) or options or rights (excluding options to purchase and rights to
subscribe for Common Stock or other securities of the Corporation convertible
into or exchangeable for Common Stock), then, in each such case, the holders of
each series of Preferred Stock shall, concurrent with the distribution to
holders of Common Stock, receive a like distribution based upon the number of
shares of Common Stock into which such series of Preferred Stock is convertible.

                    (f)  In case, at any time after the date hereof, of any
capital reorganization, or any reclassification of the stock of the Corporation
(other than as a result of a stock dividend or subdivision, split-up or
combination of shares), or the consolidation or merger of the Corporation with
or into another person (other than a consolidation or merger in which the
Corporation is the continuing entity and which does not result in any change in
the Common Stock or a consolidation or merger where Section B.2. applies), the
shares of each series of Preferred Stock shall, after such reorganization,
reclassification, consolidation, merger, sale or other disposition, be
convertible into the kind and number of shares of stock or other securities or
property of the Corporation or otherwise to which such holder would have been
entitled if immediately prior to such reorganization, reclassification,
consolidation, merger, sale or other disposition he had converted his shares of
Preferred Stock into Common Stock. The provisions of this clause (f) shall
similarly apply to successive reorganizations, reclassifications,
consolidations, mergers, sales or other dispositions.

                    (g)  All calculations under this Section C shall be made to
the nearest cent or to the nearest one one-hundredth (1/100) of a share, as the
case may be.

                    (h)  For the purpose of any computation pursuant to this
Section C.5., the "Current Market Price" at any date of one share of Common
Stock, shall be deemed to be the average of the highest reported bid and the
lowest reported offer prices on the preceding business day as furnished by the
Nasdaq National Market (or equivalent recognized source of quotations);
provided, however, that if the Common Stock is not traded in such manner that
--------  -------
the quotations referred to in this paragraph are available for the period
required hereunder, Current Market Price shall be determined in good faith by
the board of directors of the Corporation, but if challenged by the holders of
more than fifty percent (50%) of the outstanding Preferred Stock, then as
determined by an independent appraiser selected by the board of directors of the
Corporation, the cost of such appraisal to be borne by the challenging parties.

                                      -9-
<PAGE>

     6.   Minimal Adjustments.  No adjustment in the Conversion Price need be
          -------------------
made if such adjustment would result in a change in the Conversion Price of less
than $0.01. Any adjustment of less than $0.01 which is not made shall be carried
forward and shall be made at the time of and together with any subsequent
adjustment which, on a cumulative basis, amounts to an adjustment of $0.01 or
more in the Conversion Price.

     7.   No Impairment.  The Corporation will not, through any reorganization,
          -------------
recapitalization, transfer of assets, consolidation, merger, dissolution, issue
or sale of securities or any other voluntary action, avoid or seek to avoid the
observance or performance of any of the terms to be observed or performed
hereunder by the Corporation, but will at all times in good faith assist in the
carrying out of all the provisions of this Section C and in the taking of all
such action as may be necessary or appropriate in order to protect the
Conversion Rights of the holders of the Preferred Stock against impairment. This
provision shall not restrict the Corporation's right to amend its Certificate of
Incorporation with the requisite shareholder consent.

     8.   Certificate as to Adjustments.  Upon the occurrence of each
          -----------------------------
adjustment or readjustment of the Conversion Rate pursuant to this Section C,
the Corporation at its expense shall promptly compute such adjustment or
readjustment in accordance with the terms hereof and prepare and furnish to each
holder of Preferred Stock a certificate setting forth such adjustment or
readjustment and showing in detail the facts upon which such adjustment or
readjustment is based. The Corporation shall, upon written request at any time
of any holder of Preferred Stock, furnish or cause to be furnished to such
holder a like certificate setting forth (i) such adjustments and readjustments,
(ii) the Conversion Rate at the time in effect, and (iii) the number of shares
of Common Stock and the amount, if any, of other property which at the time
would be received upon the conversion of Preferred Stock.

     9.   Notices of Record Date.  In the event of any taking by the
          ----------------------
Corporation of a record of the holders of any class of securities for the
purpose of determining the holders thereof who are entitled to receive any
dividend (other than a cash dividend) or other distribution, any right to
subscribe for, purchase or otherwise acquire any shares of stock of any class or
any other securities or property or to receive any other right or upon any
Acquisition (as defined in Section B.2) or any other capital reorganization of
the Corporation, any reclassification of the capital stock, or any Liquidation,
the Corporation shall mail to each holder of Preferred Stock at least twenty
(20) days prior to such record date, a notice specifying the date on which any
such record is to be taken for the purpose of such dividend or distribution or
right or action, and the amount and character of such dividend, distribution or
right or the date such action is to be effective.

     10.  Reservation of Stock Issuable Upon Conversion.  The Corporation shall
          ---------------------------------------------
at all times reserve and keep available out of its authorized but unissued
shares of Common Stock solely for the purpose of effecting the conversion of the
shares of the Preferred Stock such number of its shares of Common Stock as shall
from time to time be sufficient to effect the full conversion of all outstanding
shares of the Preferred Stock; and if at any time the number of authorized but
unissued shares of Common Stock shall not be sufficient to effect the full
conversion of all then outstanding shares of the Preferred Stock, the
Corporation will take such corporate action as may, in the opinion of its
counsel, be necessary to increase its authorized but unissued shares of Common
Stock to such number of shares as shall be sufficient for such purpose.

                                      -10-
<PAGE>

          11.  Notices.  Any notice required by the provisions of this Section
               -------
C to be given to the holder of shares of the Preferred Stock shall be deemed
given if deposited in the United States mail, postage prepaid, and addressed to
each holder of record at his address appearing on the books of the Corporation.

     D.   Redemption.
          ----------

          1.   Restriction on Redemption.  Except as expressly provided in this
               -------------------------
Section D, the Corporation shall not have the right to redeem or otherwise
acquire for value any or all of the Preferred Stock. The redemption rights of
the Series C Preferred Stock, Series D Preferred Stock, Series E Preferred Stock
and Series F Preferred Stock shall be separate and distinct such that only the
holders of Series C Preferred Stock can effect a redemption of the Series C
Preferred Stock, only the holders of Series D Preferred Stock can effect a
redemption of the Series D Preferred Stock, only the holders of Series E
Preferred Stock can effect a redemption of the Series E Preferred Stock and only
the holders of Series F Preferred Stock can effect a redemption of the Series F
Preferred Stock.

          2.   Redemption on Demand.  In the event that holders of a majority
               --------------------
of the then outstanding Series C Preferred Stock give written notice to the
Corporation of a demand for redemption of their Series C Preferred Stock (a
"Series C Redemption Notice"), the holders of a majority of the then outstanding
Series D Preferred Stock give written notice to the Corporation of a demand for
redemption of their Series D Preferred Stock (a "Series D Redemption Notice"),
the holders of a majority of the then outstanding Series E Preferred Stock give
written notice to the Corporation of a demand for redemption of their Series E
Preferred Stock (a "Series E Redemption Notice") or the holders of a majority of
the then outstanding Series F Preferred Stock give written notice to the
Corporation of a demand for redemption of their Series F Preferred Stock (a
"Series F Redemption Notice") at any time after December 31, 2004, the
Corporation will, on the date 90 days after such notice is given (a "Redemption
Date"), to the extent legally permitted, repurchase all shares of Series C
Preferred Stock (with respect to a Series C Redemption Notice), Series D
Preferred Stock (with respect to a Series D Redemption Notice), Series E
Preferred Stock (with respect to a Series E Redemption Notice), or Series F
Preferred Stock (with respect to a Series F Redemption Notice) elected to be
redeemed by holders of Series C Preferred Stock, Series D Preferred Stock,
Series E Preferred Stock or Series F Preferred Stock, by payment of the
Redemption Price (as defined below) in three equal annual installments.

          3.   Redemption Price.  The price per share to be paid to repurchase
               ----------------
the Series C Preferred Stock, the Series D Preferred Stock, the Series E
Preferred Stock or Series F Preferred Stock shall be an amount equal to $1.30,
$1.65, $4.25 and $10.00 per share of Series C Preferred Stock, Series D
Preferred Stock, Series E Preferred Stock or Series F Preferred Stock,
respectively (as adjusted for any stock dividend, combination, splits, recaps
and the like with respect to the shares, plus a further amount equal to any
dividends declared but unpaid on such series (the "Redemption Price").

          4.   Partial Redemption.  In the event of any redemption of only a
               ------------------
part of the then outstanding Series C Preferred Stock, Series D Preferred Stock,
Series E Preferred Stock or Series F Preferred Stock, as the case may be, the
Corporation shall effect such redemption pro rata

                                      -11-
<PAGE>

among the holders of Series C Preferred Stock, Series D Preferred Stock, Series
E Preferred Stock or Series F Preferred Stock according to the aggregate
Redemption Price each such holder would otherwise be entitled to receive.

          5.   Redemption Procedure.  At least 30 days prior to the Redemption
               --------------------
Date, written notice (the "Redemption Notice") shall be mailed, postage prepaid,
to each holder of record (at the close of business on the business day next
preceding the day on which notice is given) of the Series C Preferred Stock,
Series D Preferred Stock, Series E Preferred Stock or Series F Preferred Stock
electing to have shares redeemed, at the address last shown on the records of
the Corporation for such holder or given by the holder to the Corporation for
the purpose of notice or if no such address appears or is given, at the place
where the principal executive office of the Corporation is located, notifying
such holder of the redemption to be effected, specifying the number of shares to
be redeemed, the Redemption Price, the place at which payment may be obtained
and the date on which such holder's right to convert Series C Preferred Stock,
Series D Preferred Stock, Series E Preferred Stock or Series F Preferred Stock
into Common Stock as to such shares terminates and calling upon such holder to
surrender to the Corporation, in the manner and at the place designated, its
certificate or certificates representing the shares to be redeemed. Except as
provided in Section D.6., on or after the Redemption Date, each holder of Series
C Preferred Stock, Series D Preferred Stock, Series E Preferred Stock or Series
F Preferred Stock to be redeemed shall surrender to the Corporation the
certificate or certificates representing such shares, in the manner and at the
place designated in the Redemption Notice, and thereupon, subject to the
provisions of Section D.4., the aggregate Redemption Price of such shares shall
be payable to the order of the person whose name appears on such certificate or
certificates as the owner thereof and each surrendered certificate shall be
canceled. In the event less than all the shares represented by any such
certificate are redeemed, a new certificate shall be issued representing the
unredeemed shares.

          6.   Effect of Redemption.  From and after the Redemption Date,
               --------------------
unless there shall have been a default in payment of the Redemption Price, all
rights of the holders of such shares as holders of Series C Preferred Stock,
Series D Preferred Stock, Series E Preferred Stock or Series F Preferred Stock
(except the right to receive their respective Redemption Price without interest
upon surrender of their certificate or certificates) shall cease with respect to
such shares, and such shares shall not thereafter be transferred on the books of
the Corporation or be deemed to be outstanding for any purpose whatsoever. If
the funds of the Corporation legally available for redemption of shares of
Series C Preferred Stock, Series D Preferred Stock, Series E Preferred Stock or
Series F Preferred Stock on any Redemption Date are insufficient to redeem the
total number of shares of Series C Preferred Stock, Series D Preferred Stock,
Series E Preferred Stock or Series F Preferred Stock to be redeemed on such
date, those funds which are legally available will be used to redeem the maximum
possible number of such shares pro rata as described in Section D.4. The shares
of Series C Preferred Stock, Series D Preferred Stock, Series E Preferred Stock
or Series F Preferred Stock not redeemed shall remain outstanding and be
entitled to all the rights and preferences provided herein. At any time
thereafter when additional funds of the Corporation are legally available for
the redemption of shares of Series C Preferred Stock, Series D Preferred Stock,
Series E Preferred Stock or Series F Preferred Stock, such funds will
immediately be set aside for the redemption of the balance of the shares which
the Corporation has become obligated to redeem on any Redemption Date but which
it has not redeemed; provided that the holders of such Series C

                                      -12-
<PAGE>

Preferred Stock, Series D Preferred Stock, Series E Preferred Stock or Series F
Preferred Stock shall receive at least 30 days notice of such redemption.

          7.   Redemption Funding.  On or prior to each Redemption Date, the
               ------------------
Corporation shall deposit the Redemption Price of all shares of Preferred Stock
designated for redemption in the Redemption Notice, with a bank or trust
Corporation located in the State of California having aggregate capital and
surplus in excess of $100,000,000 as a trust fund for the benefit of the
respective holders of the shares designated for redemption and not yet redeemed.
Simultaneously, the Corporation shall deposit irrevocable instructions and
authority to such bank or trust Corporation to pay, on and after the date fixed
for redemption or prior thereto, the Redemption Price of the Series C Preferred
Stock, Series D Preferred Stock, Series E Preferred Stock or Series F Preferred
Stock to the holders thereof, respectively, upon surrender of their
certificates. Any money or notes deposited by the Corporation pursuant to this
Section D.7. for the redemption of shares which are thereafter converted into
shares of Common Stock no later than the close of business on the last business
day prior to each Redemption Date shall be returned to the Corporation forthwith
upon such conversion. The balance of any money or notes deposited by the
Corporation pursuant to this subsection remaining unclaimed at the expiration of
six months following each Redemption Date shall thereafter be returned to the
Corporation, provided that the shareholder to which such money would be payable
hereunder shall be entitled, upon proof of its ownership of the Series C
Preferred Stock, Series D Preferred Stock, Series E Preferred Stock or Series F
Preferred Stock and payment of any bond requested by the Corporation, to receive
such monies but without interest from each Redemption Date.

     E.   Voting Rights.
          -------------

          1.   General.  Except as otherwise required by law or by Sections
               -------
E.2 and F hereof, the holder of each share of Common Stock issued and
outstanding shall have one vote and the holder of each share of Preferred Stock
shall be entitled to the number of votes equal to the number of shares of Common
Stock into which such share of Preferred Stock could be converted at the record
date for determination of the shareholders entitled to vote on such matters, or,
if no such record date is established, at the date such vote is taken or any
written consent of shareholders is solicited, such votes to be counted together
with all other shares of the Corporation having general voting power and not
separately as a class. Fractional votes by the holders of Preferred Stock shall
not, however, be permitted and any fractional voting rights shall (after
aggregating all shares into which shares of Preferred Stock held by each holder
could be converted) be rounded to the nearest whole number.

          2.   Election of Directors.  One (1) member of the Corporation's
               ---------------------
board of directors shall be elected by the holders of Series D Preferred Stock,
voting as a separate class, and one (1) member of the Corporation's board of
directors shall be elected by the holders of Series E Preferred Stock, voting as
a separate class. Two (2) members of the Corporation's board of directors shall
be elected by the holders of Series A Preferred Stock, Series B Preferred Stock
and Series C Preferred Stock, voting together as a single class. Two (2) members
of the Corporation's board of directors shall be elected by the holders of the
Common Stock, voting as a separate class. Any remaining members of the
Corporation's board of directors shall be elected by the holders of the Common
Stock and the Preferred Stock, voting together as a single class.

                                      -13-
<PAGE>

     Any director who was elected by a specified series, class or classes of
shares may be removed during his or her term of office, either for or without
cause, by, and only by, the affirmative vote of a majority of the holders of the
shares of the series, class or classes of shares which initially elected such
director. Such vote may be given at a special meeting of such shareholders duly
called or by an action by written consent for that purpose.

     Vacancies in the board of directors may be filled by a majority of the
remaining directors originally elected by the same series, class or classes of
shares who could elect an individual to fill such vacancy on the board of
directors, though less than a quorum, except that a vacancy created by the
removal of a director by court order may be filled by only the vote of a
majority of the outstanding shares entitled to vote thereon represented at a
duly held meeting at which a quorum is present, or by unanimous written consent
of all shares entitled to vote thereon. Each director so elected shall hold
office until the next annual meeting of shareholders and until a successor has
been elected and qualified.

     The shareholders of the specified series or class entitled to vote upon the
election of any director from which a vacancy arose may elect a director at any
time to fill such vacancy not filled by the directors.

          F.   Protective Provisions.  In addition to any other class or
               ---------------------
series vote that may be required by law, so long as at least 5,000,000 shares of
Preferred Stock shall be outstanding, the Corporation shall not without first
obtaining the approval of the holders of more than fifty percent (50%) of the
outstanding Preferred Stock:

               1.   purchase, redeem or otherwise acquire Preferred Stock other
than pursuant to the redemption provisions contained in the Certificate of
Incorporation;

               2.   repurchase any shares of Common Stock (except for the
repurchase of shares of Common Stock from directors, employees and consultants
pursuant to agreements under which the Corporation has the option to purchase
such shares at cost, not to exceed $25,000 in any twelve-month period);

               3.   authorize, issue or obligate itself to issue any security
having rights senior to or pari passu with the Series C Preferred Stock, Series
D Preferred Stock, Series E Preferred Stock or Series F Preferred Stock;

               4.   declare or pay dividends on or make any distribution on
account of the Common Stock;

               5.   effect any Liquidation or the sale of all or substantially
all of the Corporation's assets or take any action, including any merger or
consolidation, which results in the holders of the Corporation's capital stock
prior to the transaction owning less than 50% of the voting power of the
Corporation's capital stock after the transaction;

               6.   permit a subsidiary of the Corporation to sell securities to
a third party;

                                      -14-
<PAGE>

               7.   increase or decrease the number of authorized shares of
Common Stock or Preferred Stock;

               8.   amend the Certificate of Incorporation to change the rights,
preferences, privileges or limitations of the Preferred Stock;

               9.   change the variable range of the number of directors from
the current variable range of five (5) to seven (7);

               10.  increase the par value of the Common Stock; or

               11.  reissue any share of Preferred Stock acquired by the
Corporation by reason of redemption, purchase, conversion or otherwise.

          G.   Residual Rights.  All rights accruing to the outstanding shares
               ---------------
of the Corporation not expressly provided for to the contrary herein shall be
vested with the Common Stock.

          H.   No Reissuance of Preferred Stock.  No share or shares of
               --------------------------------
Preferred Stock acquired by the Corporation by reason of redemption, purchase,
conversion or otherwise shall be reissued; and, in addition, the Certificate of
Incorporation shall be appropriately amended to effect any corresponding
reduction in the Corporation's authorized stock.

                                  ARTICLE VI

          The following is applicable to the Common Stock:

          I.   Dividend Rights.  Subject to the prior rights of holders of all
               ---------------
classes of stock at the time outstanding having prior rights as to dividends,
the holders of the Common Stock shall be entitled to receive, when and as
declared by the Board of Directors, out of any assets of the Corporation legally
available therefor, such dividends as may be declared from time to time by the
Board of Directors.

          J.   Liquidation Rights.  Upon the liquidation, dissolution or
               ------------------
winding up of the Corporation, the assets of the Corporation shall be
distributed as provided in Section B of Article IV hereof.

          K.   Redemption.  The Common Stock is not redeemable.
               ----------


          L.   Voting Rights.  The holder of each share of Common Stock shall
               -------------
have the right to one vote, and shall be entitled to notice of any stockholders'
meeting in accordance with the Bylaws of the Corporation, and shall be entitled
to vote upon such matters and in such manner as may be provided by law. The
right to vote for directors shall be subject to Section E.2 of Article IV
hereof.

                                  ARTICLE VII

                                      -15-
<PAGE>

          The Corporation is to have perpetual existence.


                                 ARTICLE VIII

          In furtherance and not in limitation of the powers conferred by
statute, the Board of Directors is expressly authorized to make, alter, amend or
repeal the Bylaws of the Corporation.


                                  ARTICLE IX

          The election of directors need not be by written ballot unless the
Bylaws of the Corporation shall so provide; provided, however, that any election
                                   -------  --------
for directors must be by ballot if demanded by any stockholder at the meeting
and before the voting has begun.


                                   ARTICLE X

          To the fullest extent permitted by the Delaware General Corporation
Law as the same exists or as may hereafter be amended, a director of the
Corporation shall not be personally liable to the Corporation or its
stockholders for monetary damages for breach of fiduciary duty as a director.
The Corporation shall indemnify to the fullest extent permitted by the law, any
person made or threatened to be made a party, to any action or proceeding,
whether criminal, civil, administrative or investigative, by reason of the fact
the he or she, or his or her testator or intestate, is or was a director or
officer of the Corporation or any predecessor of the Corporation, or serves or
served at any other enterprise as a director or officer at the request of the
Corporation or any predecessor to the Corporation. Neither any amendment nor
repeal of this Article, nor the adoption of any provision of this Amended and
Restated Certificate of Incorporation inconsistent with this Article, shall
eliminate or reduce the effect of this Article in respect of any matter
occurring, or any cause of action, suit or claim that, but for this Article,
would accrue or arise, prior to such amendment, repeal or adoption of an
inconsistent provision.


                                  ARTICLE XI

          The Corporation reserves the right to amend, alter, change or repeal
any provision contained in this Amended and Restated Certificate of
Incorporation, in the manner now or hereafter prescribed by statute, and all
rights conferred upon stockholders herein are granted subject to this
reservation.


                                  ARTICLE XII

The name and mailing address of the incorporator are:

                    Pamela R. Contag, Ph.D.
                    860 Atlantic Avenue
                    Alameda, CA 94501

                                      -16-
<PAGE>

                 [Remainder of page intentionally left blank]

                                      -17-
<PAGE>

          I, THE UNDERSIGNED, being the incorporator hereinbefore named, for the
purpose of forming a Corporation pursuant to the General Corporation Law of the
State of Delaware, do make this certificate, hereby declaring and certifying,
under penalties of perjury, that this is my act and deed and the facts herein
stated are true, and accordingly have hereunto set my hand this 6th day of
November, 2000.


                                        /s/Pamela Reilly Contag
                                        ----------------------------------------
                                        Pamela R. Contag, Ph.D.,
                                        Co-Chief Executive Officer and President











   [SIGNATURE PAGE TO AMENDED AND RESTATED CERTIFICATE OF INCORPORATION OF
                             XENOGEN CORPORATION]

                                      -18-


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