Document:

<PAGE>   1
                                                                     EXHIBIT 4.1

                                     [LOGO]

                        GENENCOR INTERNATIONAL, INC. (TM)
                            Innovative by Nature(TM)

       COMMON STOCK                                      COMMON STOCK

        [NUMBER]                                           [SHARES]

INCORPORATED UNDER THE LAWS                   SEE REVERSE FOR CERTAIN CONDITIONS
  OF THE STATE OF DELAWARE

                                                               CUSIP 368709 10 1

This Certifies that

is the owner of

                              CERTIFICATE OF STOCK
             FULLY PAID AND NON-ASSESSABLE SHARES OF COMMON STOCK,
                          PAR VALUE $.01 PER SHARE, OF
Genencor International, Inc. This certificate is transferable on the books of
the Corporation in person or by duly authorized attorney upon surrender of this
certificate properly endorsed. This certificate is not valid until countersigned
by the Transfer Agent and Registrar. Witness the facsimile seal of the
Corporation and the facsimile signatures of its duly authorized officers.

Dated

                                     [SEAL]

/s/ STUART L. MELTON                              /s/ W. THOMAS MITCHELL

SECRETARY                                         PRESIDENT AND
                                                  CHIEF EXECUTIVE OFFICER

COUNTERSIGNED AND REGISTERED:
THE BANK OF NEW YORK

TRANSFER AGENT AND REGISTRAR

By:

AUTHORIZED SIGNATURE

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                          GENENCOR INTERNATIONAL, INC.

THE CORPORATION WILL FURNISH, WITHOUT CHARGE TO EACH SHAREHOLDER WHO SO
REQUESTS, A FULL STATEMENT OF THE DESIGNATION, RELATIVE RIGHTS, PREFERENCES AND
LIMITATIONS OF EACH CLASS OF STOCK AUTHORIZED TO BE ISSUED, AND A FULL STATEMENT
OF THE DESIGNATION, RELATIVE RIGHTS, PREFERENCES AND LIMITATIONS OF EACH SERIES
OF ANY CLASS OF PREFERRED STOCK AUTHORIZED TO BE ISSUED SO FAR AS THE SAME MAY
HAVE BEEN FIXED AND THE AUTHORITY OF THE BOARD TO DESIGNATE AND FIX THE RELATIVE
RIGHTS, PREFERENCES AND LIMITATIONS OF OTHER SERIES. ANY SUCH REQUEST SHOULD BE
ADDRESSED TO THE SECRETARY OF THE COMPANY, OR TO THE TRANSFER AGENT AND
REGISTRAR NAMED ON THE FACE OF THIS CERTIFICATE.

The following abbreviations, when used in the inscription on the face of this
certificate, shall be construed as though they were written out in full
according to applicable laws or regulations:

<TABLE>
<S>                                            <C>
TEN COM -   as tenants in common               UNIF GIFT MIN ACT- ____________ Custodian ____________
TEN ENT -   as tenants by the entireties                             (Cust)                (Minor)
JT TEN  -   as joint tenants with right of                        under Uniform Gifts to Minors
            survivorship and not as tenants                       Act ______________________
            in common                                                        (State)
</TABLE>

    Additional abbreviations may also be used though not in the above list.

        For value received, ___________________ hereby sell(s), assign(s) and
transfer(s) unto

PLEASE INSERT SOCIAL SECURITY OR OTHER
    IDENTIFYING NUMBER OF ASSIGNEE

______________________________________

______________________________________

________________________________________________________________________________
   PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS INCLUDING ZIP CODE OF ASSIGNEE
________________________________________________________________________________

________________________________________________________________________________

______________________________________________________________________ Shares

of the stock represented by the within Certificate, and do hereby irrevocably
constitute and appoint _________________________________________________________

________________________________________________________________________________
Attorney to transfer the said stock on the books of the within-named Corporation
with full power of substitution in the premises.

Dated _____________________________

                                        ________________________________________
                              NOTICE:   THE SIGNATURE TO THIS ASSIGNMENT MUST
                                        CORRESPOND WITH THE NAME AS WRITTEN UPON
                                        THE FACE OF THE CERTIFICATE IN EVERY
                                        PARTICULAR, WITHOUT ALTERATION OR
                                        ENLARGEMENT OR ANY CHANGE WHATEVER.

Signature(s) Guaranteed:

________________________________________
THE SIGNATURE(S) SHOULD BE GUARANTEED BY
AN ELIGIBLE GUARANTOR INSTITUTION
(BANKS, STOCKBROKERS, SAVINGS AND LOAN
ASSOCIATIONS AND CREDIT UNIONS WITH
MEMBERSHIP IN AN APPROVED SIGNATURE
GUARANTEE MEDALLION PROGRAM), PURSUANT
TO S.E.C. RULE 17Ad-15.<PAGE>   1
                                                                    EXHIBIT 10.1

                                    FORM OF

                           INDEMNIFICATION AGREEMENT

        This Agreement is made as of the ________ day of ________ 2000, by and
between Genencor International, Inc., a Delaware corporation (the "Company"),
and the undersigned [director/officer] of the Company (the "Indemnitee"), with
reference to the following facts:

        The Indemnitee is willing, under certain circumstances, to serve or
continue to serve as a [director/officer] of the Company. The Indemnitee has
indicated that he does not regard the indemnities available under the Company's
Bylaws as adequate to protect him against the risks associated with his service
to the Company. In this connection, the Company and the Indemnitee now agree
that they should enter into this Indemnification Agreement in order to provide
greater protection to Indemnitee against such risks of service to the Company.

        Section 145 of the General Corporation Law of the State of Delaware (the
"DGCL"), under which Law the Company is organized, empowers a corporation to
indemnify a person serving as a director or officer of the Company and a person
who serves at the request of the Company as a director, officer, employee or
agent of another corporation, partnership, joint venture, trust, or other
enterprise, and Section 145 of the DGCL and the Bylaws of the Company specify
that the indemnification set forth in Section 145 and in the Bylaws,
respectively, shall not be deemed exclusive of any other rights to which those
seeking indemnification may be entitled under any Bylaw, agreement, vote of
stockholders or disinterested directors or otherwise.

        In order to induce the Indemnitee to serve or continue to serve as a
[director/officer] of the Company and in consideration of his continued service,
the Company hereby agrees, as of the date first set forth above, to indemnify
the Indemnitee as follows:

               1. Indemnity. The Company will indemnify the Indemnitee, his
executors, administrators or assigns, for any Expenses (as defined below) which
the Indemnitee is or becomes legally obligated to pay in connection with any
Proceeding. As used in this Agreement the term "Proceeding" shall include any
threatened, pending or completed claim, action, suit or proceeding, whether
brought by or in the right of the Company or otherwise and whether of a civil,
criminal, administrative or investigative nature, in which the Indemnitee may be
or may have been involved as a party or otherwise, by reason of the fact that
Indemnitee is or was, or has agreed to become, a director or officer of the
Company, by reason of any actual or alleged error or misstatement or misleading
statement made or suffered by the Indemnitee, by reason of any action taken by
him or of any inaction on the Indemnitee's part while acting as such director or
officer, or by reason of the fact that such Indemnitee was serving at the
request of the Company as a director, trustee, officer, employee or agent of
another corporation, partnership, joint venture, trust or other enterprise;
provided, that in each such case Indemnitee acted in good faith and in a manner
which such Indemnitee reasonably believed to be in or not opposed to the best
interests of the Company, and, in the case of a criminal proceeding, in addition
had no reasonable cause to believe that his conduct was unlawful. As used in
this Agreement, the term "other enterprise" shall include (without limitation)
employee benefit plans and administrative committees thereof, and the term
"fines" shall include (without limitation) any excise tax assessed with respect
to any employee benefit plan.

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               2. Expenses. As used in this Agreement, the term "Expenses" shall
include (without limitation) damages, judgments, fines, penalties, settlements
and costs, attorneys' fees and disbursements and costs of attachment or similar
bonds, investigations, and any expenses of establishing a right to
indemnification under this Agreement.

               3. Enforcement. If a claim or request under this Agreement is not
paid by the Company, or on its behalf, within thirty days after a written claim
or request has been received by the Company, the Indemnitee may at any time
thereafter bring suit against the Company to recover the unpaid amount of the
claim or request and if successful in whole or in part, the Indemnitee shall be
entitled to be paid also the Expenses of prosecuting such suit. The Company
shall have the right to recoup from the Indemnitee the amount of any item or
items of Expenses theretofore paid by the Company pursuant to this Agreement, to
the extent such Expenses are not reasonable in nature or amounts; provided,
however, that the Company shall have the burden of proving such Expenses to be
unreasonable. The burden of proving that the Indemnitee is not entitled to
indemnification for any other reason shall be upon the Company.

               4. Subrogation. In the event of payment under this Agreement, the
Company shall be subrogated to the extent of such payment to all of the rights
of recovery of the Indemnitee, who shall execute all papers required and shall
do everything that may be necessary to secure such rights, including the
execution of such documents necessary to enable the Company effectively to bring
suit to enforce such rights.

               5. Exclusions. The Company shall not be liable under this
Agreement to pay any Expenses in connection with any claim made against the
Indemnitee:

                      (a) to the extent that payment is actually made to the
        Indemnitee under a valid, enforceable and collectible insurance policy;

                      (b) to the extent that the Indemnitee is indemnified and
        actually paid otherwise than pursuant to this Agreement;

                      (c) in connection with a judicial action by or in the
        right of the Company, in respect of any claim, issue or matter as to
        which the Indemnitee shall have been adjudged to be liable for
        negligence or misconduct in the performance of his duty to the Company
        unless and only to the extent that any court in which such action was
        brought shall determine upon application that, despite the adjudication
        of liability but in view of all the circumstances of the case, the
        Indemnitee is fairly and reasonably entitled to indemnity for such
        expenses as such court shall deem proper;

                      (d) with respect to proceedings or claims initiated or
        brought voluntarily by Indemnitee and not by way of defense, except with
        respect to proceedings brought to establish or enforce a right to
        indemnification under this Agreement or any other statute or law or as
        otherwise required under the DGCL, but such indemnification or
        advancement of expenses may be provided by the Company in specific cases
        if the Board has approved the initiation or bringing of such suit;

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                      (e) if it is proved by final judgment in a court of law or
        other final adjudication to have been based upon or attributable to the
        Indemnitee's in fact having gained any personal profit or advantage to
        which he was not legally entitled;

                      (f) for a disgorgement of profits made from the purchase
        and sale by the Indemnitee of securities pursuant to Section 16(b) of
        the Securities Exchange Act of 1934 and amendments thereto or similar
        provisions of any state statutory law or common law;

                      (g) brought about or contributed to by the dishonesty of
        the Indemnitee seeking payment hereunder; however, notwithstanding the
        foregoing, the Indemnitee shall be protected under this Agreement as to
        any claims upon which suit may be brought against him by reason of any
        alleged dishonesty on his part, unless a judgment or other final
        adjudication thereof adverse to the Indemnitee shall establish that he
        committed (i) acts of active and deliberate dishonesty, (ii) with actual
        dishonest purpose and intent, (iii) which acts were material to the
        cause of action so adjudicated;

                      (h) for any judgment, fine or penalty which the Company is
        prohibited by applicable law from paying as indemnity; or

                      (i) arising out of Indemnitee's breach of an employment
        agreement with the company (if any) or any other agreement with the
        Company or any of its subsidiaries.

               6. Indemnification of Expenses of Successful Party.
Notwithstanding any other provision of this Agreement, to the extent that the
Indemnitee has been successful on the merits or otherwise in defense of any
Proceeding or in defense of any claim, issue or matter therein, including
dismissal without prejudice, Indemnitee shall be indemnified against any and all
Expenses incurred in connection therewith.

               7. Partial Indemnification. If the Indemnitee is entitled under
any provision of this Agreement to indemnification by the Company for some or a
portion of Expenses, but not, however, for the total amount thereof, the Company
shall nevertheless indemnify the Indemnitee for the portion of such Expenses to
which the Indemnitee is entitled.

               8. Advance of Expenses. Expenses incurred by the Indemnitee in
connection with any Proceeding, except the amount of any settlement, shall be
paid by the Company in advance upon request of the Indemnitee that the Company
pay such Expenses; provided, however, that, if the DGCL requires that an
advancement of expenses incurred by an Indemnitee in his capacity as a director
or officer (and not in any other capacity in which service was or is rendered by
such Indemnitee, including, without limitation, service to an employee benefit
plan) shall be made only upon delivery to the Company of an undertaking (an
"Undertaking"), by or on behalf of such Indemnitee, to repay all amounts so
advanced if it shall ultimately be determined by final judicial decision from
which there is no further right to appeal that such Indemnitee is not entitled
to be indemnified for such expenses, then Indemnitee shall provide such
Undertaking.

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               9. Assumption of Defense. In the event the Company shall be
obligated to pay the expenses of any proceeding against the Indemnitee under
this Agreement, the Company, if appropriate, shall be entitled to assume the
defense of such proceeding with counsel approved by Indemnitee which approval
shall not be unreasonably withheld, upon the delivery to Indemnitee of written
notice of its election to do so. After delivery of such notice, approval of such
counsel by Indemnitee and the retention of such counsel by the Company, the
Company will not be liable to Indemnitee under this Agreement for any fees of
counsel subsequently incurred by Indemnitee with respect to the same proceeding,
unless (i) the employment of counsel by Indemnitee is authorized by the Company,
(ii) Indemnitee shall have reasonably concluded, based upon written advice of
counsel, that there may be a conflict of interest of such counsel retained by
the Company between the Company and Indemnitee in the conduct of such defense,
or (iii) the Company ceases or terminates the employment of such counsel with
respect to the defense of such proceeding, in any of which events then the fees
and expenses of Indemnitee's counsel shall be at the expense of the Company. At
all times, Indemnitee shall have the right to employ other counsel in any such
proceeding at Indemnitee's expense, and to participate in the defense of the
proceeding or claim through such counsel.

               10. Attorneys' Fees. In the event that any action is instituted
by Indemnitee under this Agreement to enforce or interpret any of the terms
hereof, Indemnitee shall be entitled to be paid all court costs and expenses,
including reasonable attorneys' fees, incurred by Indemnitee with respect to
such action, unless as a part of such action, the court of competent
jurisdiction determines that the action was not instituted in good faith or was
frivolous. In the event of an action instituted by or in the name of the Company
under this Agreement, Indemnitee shall be entitled to be paid all court costs
and expenses, including attorneys' fees, incurred by Indemnitee in defense of
such action (including with respect to Indemnitee's counterclaims and
cross-claims made in such action), unless as a part of such action the court
determines that Indemnitee's defenses to such action were not made in good faith
or were frivolous.

               11. Officer and Director Liability Insurance. The Company shall,
from time to time, make the good faith determination whether or not it is
practicable for the Company to obtain and maintain a policy or policies of
insurance with reputable insurance companies providing the officers and
directors of the Company with coverage for losses from wrongful acts, or to
ensure the Company's performance of its indemnification obligations under this
Agreement. Among other considerations, the Company will weigh the costs of
obtaining such insurance coverage against the protection afforded by such
coverage. Notwithstanding the foregoing, the Company shall have no obligation to
obtain or maintain such insurance if the Company determines in good faith that
such insurance is not reasonably available, or if the premium costs for such
insurance are disproportionate to the amount of coverage provided, if the
coverage provided by such insurance is limited by exclusions so as to provide an
insufficient indemnity.

               12. Notice of Claim. The Indemnitee, as a condition precedent to
his right to be indemnified under this Agreement, shall give to the Company
notice in writing as soon as practicable of any claim made against him for which
indemnity will or could be sought under this Agreement. Notice to the Company
shall be given at its principal office and shall be directed

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<PAGE>   5

to the Corporate Secretary (or such other address as the Company shall designate
in writing to the Indemnitee); notice shall be deemed received if sent by
prepaid mail properly addressed, the date of such notice being the date
postmarked. In addition, the Indemnitee shall give the Company such information
and cooperation as it may reasonably require and as shall be within the
Indemnitee's power.

               13. Entire Agreement. This Agreement constitutes the entire
agreement and supersedes all prior agreements and understandings, both written
and oral, among the parties with respect to the subject matter hereof and is not
intended to confer upon any person other than the parties hereto any rights or
remedies hereunder.

               14. Counterparts. This Agreement may be executed in any number of
counterparts, all of which taken together shall constitute one instrument.

               15. Indemnification Hereunder Not Exclusive. Nothing herein shall
be deemed to diminish or otherwise restrict the Indemnitee's right to
indemnification under any provision of the Certificate of Incorporation or
Bylaws of the Company and amendments thereto or under law.

               16. Governing Law. This Agreement shall be governed by and
construed in accordance with Delaware law, without regard to the conflicts of
law provisions thereof.

               17. Saving Clause. Wherever there is conflict between any
provision of this Agreement and any applicable present or future statute, law or
regulation contrary to which the Company and the Indemnitee have no legal right
to contract, the latter shall prevail, but in such event the affected provisions
of this Agreement shall be curtailed and restricted only to the extent necessary
to bring them within applicable legal requirements.

               18. Coverage. The provisions of this Agreement shall apply with
respect to the Indemnitee's service as a [director/officer] of the Company prior
to the date of this Agreement and with respect to all periods of such service
after the date of this Agreement, even though the Indemnitee may have ceased to
be a [director/officer] of the Company.

               19. Gender; Number. The use of the masculine gender shall include
the feminine. The use of the plural shall include the singular and the use of
the singular shall include the plural, as the context may require or permit.

                            (Signature Page Follows)

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        IN WITNESS WHEREOF, the parties hereto have caused this Agreement to be
duly executed and signed as of the day and year first above written.

                                        GENENCOR INTERNATIONAL, INC.

                                        By
                                           -------------------------------------

                                               Authorized Officer

                                        "INDEMNITEE"

                                        ----------------------------------------
                                        Name:

                                      S-1

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