Document:

<PAGE>   1

                                                                   EXHIBIT 10.12

        THIS WARRANT AND THE SHARES ISSUABLE HEREUNDER HAS NOT BEEN REGISTERED
        UNDER THE SECURITIES ACT OF 1933, AS AMENDED OR ANY STATE SECURITIES
        LAWS. NO SALE OR DISPOSITION MAY BE EFFECTED WITHOUT (i) EFFECTIVE
        REGISTRATION STATEMENTS RELATED THERETO, (ii) AN OPINION OF COUNSEL OR
        OTHER EVIDENCE, REASONABLY SATIS-FACTORY TO THE COMPANY, THAT SUCH
        REGISTRATIONS ARE NOT REQUIRED, (iii) RECEIPT OF NO-ACTION LETTERS FROM
        THE APPROPRIATE GOVERN-MENTAL AUTHORITIES, OR (iv) OTHERWISE COMPLYING
        WITH THE PROVISIONS OF SECTION 7 OF THIS WARRANT.

                          SIGNAL PHARMACEUTICALS, INC.

                       WARRANT TO PURCHASE 250,000 SHARES
                          OF SERIES C-1 PREFERRED STOCK

        THIS CERTIFIES THAT, for value received, MMC/GATX PARTNERSHIP NO. I and
its assignees are entitled to subscribe for and purchase 250,000 shares of the
fully paid and nonassessable Series C-1 Preferred Stock (as adjusted pursuant to
Section 4 hereof, the "Shares") of SIGNAL PHARMACEUTICALS, INC., a California
corporation (the "Company"), at the price of $2.10 per share (such price and
such other price as shall result, from time to time, from the adjustments
specified in Section 4 hereof is herein referred to as the "Warrant Price"),
subject to the provisions and upon the terms and conditions hereinafter set
forth. As used herein, (a) the term "Series Preferred" shall mean the Company's
presently authorized Series C-1 Preferred Stock, and any stock into or for which
such Series C-1 Preferred Stock may hereafter be converted or exchanged, (b) the
term "Date of Grant" shall mean November 22, 1996, and (c) the term "Other
Warrants" shall mean any other warrants issued by the Company in connection with
the transaction with respect to which this Warrant was issued, and any warrant
issued upon transfer or partial exercise of this Warrant. The term "Warrant" as
used herein shall be deemed to include Other Warrants unless the context clearly
requires otherwise.

        1. Term. The purchase right represented by this Warrant is exercisable,
in whole or in part, at any time and from time to time from the Date of Grant
through the tenth anniversary of the Date of Grant; provided, however, that if
the Company's initial public offering ("IPO") of its Common Stock effected
pursuant to a Registration Statement on Form S-1 or Form SB-2 (or their
respective successors) filed under the Securities Act of 1933, as amended (the
"Act") occurs after the fifth anniversary of the Date of Grant and prior to the
tenth anniversary of the Date of Grant, then this Warrant shall be exercisable
through the fifth anniversary of the effective date of such initial public
offering.

        2. Method of Exercise; Payment; Issuance of New Warrant. Subject to
Section 1 hereof, the purchase right represented by this Warrant may be
exercised by the holder hereof, in whole or in part and from time to time, at
the election of the holder hereof, by (a) the surrender of this Warrant (with
the notice of exercise substantially in the form attached hereto as Exhibit A
duly completed and executed) at the principal office of the Company and by the
payment to the Company, by certified or bank check, or by wire transfer to an
account designated by the Company (a "Wire Transfer") of an amount equal to the
then applicable Warrant Price multiplied by the number of Shares then being
purchased, or (b) if in connection with a registered public offering of the
Company's securities, the surrender of this Warrant (with the notice of exercise
form attached hereto as Exhibit A-1 duly completed and executed) at the
principal office of the Company together with notice of arrangements reasonably
satisfactory to the Company for payment to the Company either by certified or
bank check or by Wire Transfer from the proceeds of the sale of shares to be
sold by the holder in such public offering of an amount equal to the then
applicable Warrant Price per

<PAGE>   2

share multiplied by the number of Shares then being purchased by the holder
hereof or (c) exercise of the right provided for in Section 10.3 hereof. The
person or persons in whose name(s) any certificate(s) representing shares of
Series Preferred shall be issuable upon exercise of this Warrant shall be deemed
to have become the holder(s) of record of, and shall be treated for all purposes
as the record holder(s) of, the shares represented thereby (and such shares
shall be deemed to have been issued) immediately prior to the close of business
on the date or dates upon which this Warrant is exercised. In the event of any
exercise of the rights represented by this Warrant, certificates for the shares
of stock so purchased shall be delivered to the holder hereof as soon as
possible and in any event within thirty (30) days after such exercise and,
unless this Warrant has been fully exercised or expired, a new Warrant
representing the portion of the Shares, if any, with respect to which this
Warrant shall not then have been exercised shall also be issued to the holder
hereof as soon as possible and in any event within such thirty-day period.

        3. Stock Fully Paid; Reservation of Shares. All Shares that may be
issued upon the exercise of the rights represented by this Warrant will, upon
issuance pursuant to the terms and conditions herein, be fully paid and
nonassessable, and free from all taxes, liens and charges with respect to the
issue thereof. During the period within which the rights represented by this
Warrant may be exercised, the Company will at all times have authorized, and
reserved for the purpose of the issue upon exercise of the purchase rights
evidenced by this Warrant, a sufficient number of shares of its Series Preferred
to provide for the exercise of the rights represented by this Warrant and a
sufficient number of shares of its Common Stock to provide for the conversion of
the Series Preferred into Common Stock.

        4. Adjustment of Warrant Price and Number of Shares. The number and kind
of securities purchasable upon the exercise of this Warrant and the Warrant
Price shall be subject to adjustment from time to time upon the occurrence of
certain events, as follows:

               (a) Reclassification or Merger. In case of any reclassification
or change of securities of the class issuable upon exercise of this Warrant
(other than a change in par value, or from par value to no par value, or from no
par value to par value, or as a result of a subdivision or combination), or in
case of any merger of the Company with or into another corporation (other than a
merger with another corporation in which the Company is the acquiring and the
surviving corporation and which does not result in any reclassification or
change of outstanding securities issuable upon exercise of this Warrant), or in
case of any sale of all or substantially all of the assets of the Company, the
Company, or such successor or purchasing corporation, as the case may be, shall
duly execute and deliver to the holder of this Warrant a new Warrant with a term
ending on the same date as specified for this Warrant (in form and substance
satisfactory to the holder of this Warrant), so that the holder of this Warrant
shall have the right to receive, at a total purchase price not to exceed that
payable upon the exercise of the unexercised portion of this Warrant, and in
lieu of the shares of Series Preferred theretofore issuable upon exercise of
this Warrant, the kind and amount of shares of stock, other securities, money
and property receivable upon such reclassification, change or merger by a holder
of the number of shares of Series Preferred purchasable under this Warrant
immediately prior to such reclassification, change or merger. Such new Warrant
shall provide for adjustments that shall be as nearly equivalent as may be
practicable to the adjustments provided for in this Section 4 and, in the case
of a new Warrant issuable after conversion of the authorized shares of the
Series Preferred into shares of Common Stock or after the amendment of the terms
of the antidilution protection of the Series Preferred, shall provide for
antidilution protection that shall be as nearly equivalent as may be practicable
to the antidilution provisions applicable to the Series Preferred on the Date of
Grant. The provisions of this subparagraph (a) shall similarly apply to
successive reclassifications, changes, mergers and transfers.

                                      -2-
<PAGE>   3

Notwithstanding the foregoing, such antidilution protection shall in no event
provide superior rights, preferences and privileges with regard to the Series
Preferred than the antidilution protection accorded to any then currently
designated series of preferred stock.

               (b) Subdivision or Combination of Shares. If the Company at any
time while this Warrant remains outstanding and unexpired shall subdivide or
combine its outstanding shares of Series Preferred, the Warrant Price shall be
proportionately decreased in the case of a subdivision or increased in the case
of a combination, effective at the close of business on the date the subdivision
or combination becomes effective.

               (c) Stock Dividends and Other Distributions. If the Company at
any time while this Warrant is outstanding and unexpired shall (i) pay a
dividend with respect to Series Preferred payable in Series Preferred, or (ii)
make any other distribution with respect to Series Preferred (except any
distribution specifically provided for in Sections 4(a) and 4(b)), of Series
Preferred, then the Warrant Price shall be adjusted, from and after the date of
determination of shareholders entitled to receive such dividend or distribution,
to that price determined by multiplying the Warrant Price in effect immediately
prior to such date of determination by a fraction (i) the numerator of which
shall be the total number of shares of Series Preferred outstanding immediately
prior to such dividend or distribution, and (ii) the denominator of which shall
be the total number of shares of Series Preferred outstanding immediately after
such dividend or distribution.

               (d) Adjustment of Number of Shares. Upon each adjustment in the
Warrant Price, the number of Shares of Series Preferred purchasable hereunder
shall be adjusted, to the nearest whole share, to the product obtained by
multiplying the number of Shares purchasable immediately prior to such
adjustment in the Warrant Price by a fraction, the numerator of which shall be
the Warrant Price immediately prior to such adjustment and the denominator of
which shall be the Warrant Price immediately thereafter.

               (e) Antidilution Rights. The other antidilution rights applicable
to the Shares of Series Preferred purchasable hereunder are set forth in the
Company's Articles of Incorporation, as amended through the Date of Grant, a
true and complete copy of which is attached hereto as Exhibit B (the "Charter").
Such antidilution rights shall not be restated, amended, modified or waived in
any manner which would adversely affect the Series Preferred relative to any
other currently designated series of the Company's preferred stock without such
holder's prior written consent. The Company shall promptly provide the holder
hereof with any restatement, amendment, modification or waiver of the Charter
promptly after the same has been made.

        5. Notice of Adjustments. Whenever the Warrant Price or the number of
Shares purchasable hereunder shall be adjusted pursuant to Section 4 hereof, the
Company shall make a certificate signed by its chief financial officer setting
forth, in reasonable detail, the event requiring the adjustment, the amount of
the adjustment, the method by which such adjustment was calculated, and the
Warrant Price and the number of Shares purchasable hereunder after giving effect
to such adjustment, and shall cause copies of such certificate to be mailed
(without regard to Section 13 hereof, by first class mail, postage prepaid) to
the holder of this Warrant. In addition, whenever the conversion price or
conversion ratio of the Series Preferred shall be adjusted, the Company shall
make a certificate signed by its chief financial officer setting forth, in
reasonable detail, the event requiring the adjustment, the amount of the
adjustment, the method by

                                      -3-
<PAGE>   4

which such adjustment was calculated, and the conversion price or ratio of the
Series Preferred after giving effect to such adjustment, and shall cause copies
of such certificate to be mailed (without regard to Section 13 hereof, by first
class mail, postage prepaid) to the holder of this Warrant.

        6. Fractional Shares. No fractional shares of Series Preferred will be
issued in connection with any exercise hereunder, but in lieu of such fractional
shares the Company shall make a cash payment therefor based on the fair market
value of the Series Preferred on the date of exercise as reasonably determined
in good faith by the Company's Board of Directors.

        7. Compliance with Act; Disposition of Warrant or Shares of Series
Preferred.

               (a) Compliance with Act. The holder of this Warrant, by
acceptance hereof, agrees that this Warrant, and the shares of Series Preferred
to be issued upon exercise hereof and any Common Stock issued upon conversion
thereof are being acquired for investment and that such holder will not offer,
sell or otherwise dispose of this Warrant, or any shares of Series Preferred to
be issued upon exercise hereof or any Common Stock issued upon conversion
thereof except under circumstances which will not result in a violation of the
Act or any applicable state securities laws. Upon exercise of this Warrant,
unless the Shares being acquired are registered under the Act and any applicable
state securities laws or an exemption from such registration is available, the
holder hereof shall confirm in writing that the shares of Series Preferred so
purchased (and any shares of Common Stock issued upon conversion thereof) are
being acquired for investment and not with a view toward distribution or resale
in violation of the Act or applicable state securities laws and shall confirm
such other matters related thereto as may be reasonably requested by the
Company. This Warrant and all shares of Series Preferred issued upon exercise of
this Warrant and all shares of Common Stock issued upon conversion thereof
(unless registered under the Act and any applicable state securities laws) shall
be stamped or imprinted with a legend in the following form:

"THESE SECURITIES HAVE NOT BEEN REGISTERED UNDER THE SECURITIES ACT OF 1933, AS
AMENDED, OR ANY STATE SECURITIES LAWS. THEY MAY NOT BE SOLD, OFFERED FOR SALE,
PLEDGED OR HYPOTHECATED IN THE ABSENCE OF A REGISTRATION STATEMENT IN EFFECT
WITH RESPECT TO THE SECURITIES UNDER SUCH ACT OR AN OPINION OF COUNSEL
SATISFACTORY TO THE COMPANY THAT SUCH REGISTRATION IS NOT REQUIRED OR UNLESS
SOLD PURSUANT TO RULE 144 OF SUCH ACT OR OTHERWISE COMPLYING WITH THE PROVISIONS
OF SECTION 7 OF THE WARRANT UNDER WHICH THESE SECURITIES WERE ISSUED, DIRECTLY
OR INDIRECTLY."

        Said legend shall be removed by the Company, upon the request of a
holder, at such time as the restrictions on the transfer of the applicable
security shall have terminated. In addition, in connection with the issuance of
this Warrant, the holder specifically represents to the Company by acceptance of
this Warrant as follows:

        (1) The holder is aware of the Company's business affairs and financial
condition, and has acquired information about the Company sufficient to reach an
informed and knowledgeable decision to acquire this Warrant. The holder is
acquiring this Warrant for its own account for investment purposes only and not
with a view to, or for the resale in connection with, any "distribution" thereof
in violation of the Act, and the holder has no present intention of selling or
engaging in any public distribution of the same except pursuant to registration
under the Act or exemption therefrom.

                                      -4-
<PAGE>   5

        (2) The holder understands that this Warrant has not been registered
under the Act in reliance upon a specific exemption therefrom, which exemption
depends upon, among other things, the bona fide nature of the holder's
investment intent as expressed herein.

        (3) The holder is an "accredited investor" within the meaning of Rule
501 of Regulation D promulgated under the Act.

        (4) The holder acknowledges that investment in this Warrant and the
Shares to issued upon exercise hereof involves a high degree of risk and
represents that it is able, without materially impairing its financial condition
to hold this Warrant and such Shares for an indefinite period of time and to
suffer a complete loss of its investment.

        (5) The holder further understands that this Warrant must be held
indefinitely unless subsequently registered under the Act and qualified under
any applicable state securities laws, or unless exemptions from registration and
qualification are otherwise available. The holder is aware of the provisions of
Rule 144, promulgated under the Act.

               (b) Disposition of Warrant or Shares. With respect to any offer,
sale or other disposition of this Warrant or any shares of Series Preferred
acquired pursuant to the exercise of this Warrant prior to registration of such
Warrant or shares, the holder hereof agrees to give written notice to the
Company prior thereto, describing briefly the manner thereof, together with a
written opinion of such holder's counsel, or other evidence, if reasonably
requested by the Company, to the effect that such offer, sale or other
disposition may be effected without registration or qualification (under the Act
as then in effect or any federal or state securities law then in effect) of this
Warrant or such shares of Series Preferred or Common Stock and indicating
whether or not under the Act certificates for this Warrant or such shares of
Series Preferred to be sold or otherwise disposed of require any restrictive
legend as to applicable restrictions on transferability in order to ensure
compliance with such law. Promptly upon receiving such written notice and
reasonably satisfactory opinion or other evidence, if so requested, the Company,
as promptly as practicable but no later than fifteen (15) days after receipt of
the written notice, shall notify such holder that such holder may sell or
otherwise dispose of this Warrant or such shares of Series Preferred or Common
Stock, all in accordance with the terms of the notice delivered to the Company.
If a determination has been made pursuant to this Section 7(b) that the opinion
of counsel for the holder or other evidence is not reasonably satisfactory to
the Company, the Company shall so notify the holder promptly with details
thereof after such determination has been made. Notwithstanding the foregoing,
this Warrant or such shares of Series Preferred or Common Stock may, as to such
federal laws, be offered, sold or otherwise disposed of in accordance with Rule
144 or 144A under the Act, provided that the Company shall have been furnished
with such information as the Company may reasonably request to provide a
reasonable assurance that the provisions of Rule 144 or 144A have been
satisfied. Each certificate representing this Warrant or the shares of Series
Preferred thus transferred (except a transfer pursuant to Rule 144 or 144A)
shall bear a legend as to the applicable restrictions on transferability in
order to ensure compliance with such laws, unless in the aforesaid opinion of
counsel for the holder as approved by the Company, such legend is not required
in order to ensure compliance with such laws. The Company may issue stop
transfer instructions to its transfer agent in connection with such
restrictions.

               (c) Applicability of Restrictions. Neither any restrictions of
any legend described in this Warrant nor the requirements of Section 7(b) above
shall apply to any transfer of, or grant of a security

                                      -5-
<PAGE>   6

interest in, this Warrant (or the Series Preferred or Common Stock obtainable
upon exercise thereof) or any part hereof (i) to a partner of the holder if the
holder is a partnership, (ii) to a partnership of which the holder is a partner,
or (iii) to any affiliate of the holder if the holder is a corporation;
provided, however, in any such transfer, if applicable, the transferee shall
agree in writing to be bound by the terms of this Warrant as if an original
signatory hereto.

        8. Rights as Shareholders; Information. No holder of this Warrant, as
such, shall be entitled to vote or receive dividends or be deemed the holder of
Series Preferred or any other securities of the Company which may at any time be
issuable on the exercise hereof for any purpose, nor shall anything contained
herein be construed to confer upon the holder of this Warrant, as such, any of
the rights of a shareholder of the Company or any right to vote for the election
of directors or upon any matter submitted to shareholders at any meeting
thereof, or to receive notice of meetings, or to receive dividends or
subscription rights or otherwise until this Warrant shall have been exercised
and the Shares purchasable upon the exercise hereof shall have become
deliverable, as provided herein. Notwithstanding the foregoing, the Company will
transmit to the holder of this Warrant such information, documents and reports
(i) as set forth on Exhibit C attached hereto prior to the Company's IPO and
(ii) as are generally distributed to the holders of any class or series of the
securities of the Company concurrently with the distribution thereof to the
shareholders after the Company's IPO.

        9. Registration Rights. The Company grants registration rights to the
holder of this Warrant for any Common Stock of the Company obtained upon
conversion of the Series Preferred, that are the same as the registration rights
granted to the investors in that certain Amended and Restated Investors' Rights
Agreement dated as of March 31, 1996 (the "Registration Rights Agreement"), with
the following exceptions and clarifications:

                (1)     The holder will have no demand registration rights as
                        set forth in Section 1.2 of the Registration Rights
                        Agreement.

                (2)     The holder will be subject to the same provisions
                        regarding indemnification as contained in the
                        Registration Rights Agreement.

                (3)     The registration rights are assignable by the holder of
                        this Warrant to the extent such assignment is not
                        inconsistent with Section 7 hereof and Section 1.13 of
                        the Registration Rights Agreement.

                (4)     The holder shall be subject to the "Market Stand-off"
                        provisions of Section 1.15 of the Registration Rights
                        Agreement.

        10. Additional Rights.

        10.1 Secondary Sales. The Company will promptly provide the holder of
this Warrant with notice of any offer (of which it has knowledge) to acquire
from the Company's security holders more than ten percent (10%) of the total
voting power of the Company.

        10.2 Mergers. The Company shall provide the holder of this Warrant with
at least twenty (20) days' notice of the terms and conditions of any of the
following potential transactions: (i) the sale, lease,

                                      -6-
<PAGE>   7

exchange, conveyance or other disposition of all or substantially all of the
Company's property or business, or (ii) its merger into or consolidation with
any other corporation (other than a wholly-owned subsidiary of the Company), or
any transaction (including a merger or other reorganization) or series of
related transactions, in which more than 50% of the voting power of the Company
is disposed of.

        10.3  Right to Convert Warrant into Stock:  Net Issuance.

               (a) Right to Convert. In addition to and without limiting the
rights of the holder under the terms of this Warrant, the holder shall have the
right to convert this Warrant or any portion thereof (the "Conversion Right")
into shares of Series Preferred (or Common Stock if the Series Preferred has
been converted into Common Stock) as provided in this Section 10.3 at any time
or from time to time during the term of this Warrant. Upon exercise of the
Conversion Right with respect to a particular number of shares subject to this
Warrant (the "Converted Warrant Shares"), the Company shall deliver to the
holder (without payment by the holder of any exercise price or any cash or other
consideration) (X) that number of shares of fully paid and nonassessable Series
Preferred (or Common Stock if the Series Preferred has been converted into
Common Stock) equal to the quotient obtained by dividing the value of this
Warrant (or the specified portion hereof) on the Conversion Date (as defined in
subsection (b) hereof), which value shall be determined by subtracting (A) the
aggregate Warrant Price of the Converted Warrant Shares immediately prior to the
exercise of the Conversion Right from (B) the aggregate fair market value of the
Converted Warrant Shares issuable upon exercise of this Warrant (or the
specified portion hereof) on the Conversion Date (as herein defined) by (Y) the
fair market value of one share of Series Preferred (or Common Stock if the
Series Preferred has been converted into Common Stock) on the Conversion Date
(as herein defined).

        Expressed as a formula, such conversion (assuming the Series Preferred
has been converted into Common Stock) shall be computed as follows:

        X = B - A
            -----
              Y

        Where:   X  =  the number of shares of Common Stock that may
                       be issued to holder

                 Y  =  the fair market value of one share of Common Stock

                 A  =  the aggregate Warrant Price (i.e., Converted
                       Warrant Shares x Warrant Price)

                 B  =  the aggregate fair market value (i.e., fair market
                       value x Converted Warrant Shares)

        No fractional shares shall be issuable upon exercise of the Conversion
Right, and, if the number of shares to be issued determined in accordance with
the foregoing formula is other than a whole number, the Company shall pay to the
holder an amount in cash equal to the fair market value of the resulting
fractional share on the Conversion Date (as hereinafter defined). For purposes
of Section 9 of this Warrant, shares

                                      -7-
<PAGE>   8

issued pursuant to the Conversion Right shall be treated as if they were issued
upon the exercise of this Warrant.

               (b) Method of Exercise. The Conversion Right may be exercised by
the holder by the surrender of this Warrant at the principal office of the
Company together with a written statement specifying that the holder thereby
intends to exercise the Conversion Right and indicating the number of shares
subject to this Warrant which are being surrendered (referred to in Section
10.3(a) hereof as the Converted Warrant Shares) in exercise of the Conversion
Right. Such conversion shall be effective upon receipt by the Company of this
Warrant together with the aforesaid written statement, or on such later date as
is specified therein (the "Conversion Date"), and, at the election of the holder
hereof, may be made contingent upon the closing of the sale of the Company's
Common Stock to the public in a public offering pursuant to a Registration
Statement under the Act (a "Public Offering"). Certificates for the shares
issuable upon exercise of the Conversion Right and, if applicable, a new warrant
evidencing the balance of the shares remaining subject to this Warrant, shall be
issued as of the Conversion Date and shall be delivered to the holder within
thirty (30) days following the Conversion Date. Any conversion from Series
Preferred to Common Stock shall be in the ratio of one (1) share of Common Stock
for each share of Series Preferred (as adjusted herein and in the Charter). On
the Date of Grant, each share of the Series Preferred represented by this
Warrant is convertible into one share of Common Stock.

               (c) Determination of Fair Market Value. For purposes of this
Section 10.3, "fair market value" of a share of Series Preferred (or Common
Stock if the Series Preferred has been automatically converted into Common
Stock) as of a particular date (the "Determination Date") shall mean:

                        (i) If the Conversion Right is exercised in connection
with and contingent upon a Public Offering, and if the Company's Registration
Statement relating to such Public Offering ("Registration Statement") has been
declared effective by the SEC, then the initial "Price to Public" specified in
the final prospectus with respect to such offering.

                        (ii) If the Conversion Right is not exercised in
connection with and contingent upon a Public Offering, then as follows:

               (A) If traded on a securities exchange, the fair market value of
        the Common Stock shall be deemed to be the average of the closing prices
        of the Common Stock on such exchange over the 30-day period ending five
        business days prior to the Determination Date, and the fair market value
        of the Series Preferred shall be deemed to be such fair market value of
        the Common Stock multiplied by the number of shares of Common Stock into
        which each share of Series Preferred is then convertible;

               (B) If traded over-the-counter, the fair market value of the
        Common Stock shall be deemed to be the average of the closing bid prices
        of the Common Stock over the 30-day period ending five business days
        prior to the Determination Date, and the fair market value of the Series
        Preferred shall be deemed to be such fair market value of the Common
        Stock multiplied by the number of shares of Common Stock into which each
        share of Series Preferred is then convertible; and

                                      -8-
<PAGE>   9

               (C) If there is no public market for the Common Stock, then fair
        market value shall be determined in good faith by the Company' Board of
        Directors.

               10.4 Exercise Prior to Expiration. To the extent this Warrant is
not previously exercised as to all of the Shares subject hereto, and if the fair
market value of one share of the Series Preferred is greater than the Warrant
Price then in effect, this Warrant shall be deemed automatically exercised
pursuant to Section 10.3 above (even if not surrendered) immediately before its
expiration. For purposes of such automatic exercise, the fair market value of
one share of the Series Preferred upon such expiration shall be determined
pursuant to Section 10.3(c). To the extent this Warrant or any portion thereof
is deemed automatically exercised pursuant to this Section 10.4, the Company
agrees to promptly notify the holder hereof of the number of Shares, if any, the
holder hereof is to receive by reason of such automatic exercise.

        11. Representations and Warranties. The Company represents and warrants
to the holder of this Warrant as follows:

               (a) This Warrant has been duly authorized and executed by the
Company and is a valid and binding obligation of the Company enforceable in
accordance with its terms, subject to laws of general application relating to
bankruptcy, insolvency and the relief of debtors and the rules of law or
principles at equity governing specific performance, injunctive relief and other
equitable remedies;

               (b) The Shares have been duly authorized and reserved for
issuance by the Company and, when issued in accordance with the terms hereof,
will be validly issued, fully paid and non-assessable;

               (c) The rights, preferences, privileges and restrictions granted
to or imposed upon the Series Preferred and the holders thereof are as set forth
in the Charter, as amended to the Date of the Grant, a true and complete copy of
which has been delivered to the original holder of this Warrant and is attached
hereto as Exhibit B;

               (d) The shares of Common Stock issuable upon conversion of the
Shares have been duly authorized and reserved for issuance by the Company and,
when issued in accordance with the terms of the Charter will be validly issued,
fully paid and nonassessable;

               (e) The execution and delivery of this Warrant are not, and the
issuance of the Shares upon exercise of this Warrant in accordance with the
terms hereof will not be, inconsistent with the Company's Charter or by-laws, do
not and will not contravene any law, governmental rule or regulation, judgment
or order applicable to the Company, and do not and will not conflict with or
contravene any provision of, or constitute a default under, any indenture,
mortgage, contract or other instrument of which the Company is a party or by
which it is bound or require the consent or approval of, the giving of notice
to, the registration or filing with or the taking of any action in respect of or
by, any Federal, state or local government authority or agency or other person,
except for the filing of notices pursuant to federal and state securities laws,
which filings will be effected by the time required thereby; and

               (f) There are no actions, suits, audits, investigations or
proceedings pending or, to the knowledge of the Company, threatened against the
Company in any court or before any governmental commission, board or authority
which, if adversely determined, will have a material adverse effect on the
ability of the Company to perform its obligations under this Warrant.

                                      -9-
<PAGE>   10

        12. Modification and Waiver. This Warrant and any provision hereof may
be changed, waived, discharged or terminated only by an instrument in writing
signed by the party against which enforcement of the same is sought.

        13. Notices. Any notice, request, communication or other document
required or permitted to be given or delivered to the holder hereof or the
Company shall be delivered, or shall be sent by certified or registered mail,
postage prepaid, to each such holder at its address as shown on the books of the
Company or to the Company at the address indicated therefor on the signature
page of this Warrant.

        14. Binding Effect on Successors. This Warrant shall be binding upon any
corporation succeeding the Company by merger, consolidation or acquisition of
all or substantially all of the Company's assets, and the obligations of the
Company set forth in Section 8 hereof and the rights, preferences and privileges
set forth in the Charter relating to the Series Preferred issuable upon the
exercise or conversion of this Warrant shall survive the exercise, conversion
and termination of this Warrant and all of the covenants and agreements of the
Company shall inure to the benefit of the successors and assigns of the holder
hereof. The Company will, at the time of the exercise or conversion of this
Warrant, in whole or in part, upon request of the holder hereof but at the
Company's expense, acknowledge in writing its continuing obligation to the
holder hereof in respect of any rights (including, without limitation, any right
to registration of the Shares) to which the holder hereof shall continue to be
entitled after such exercise or conversion in accordance with this Warrant;
provided, that the failure of the holder hereof to make any such request shall
not affect the continuing obligation of the Company to the holder hereof in
respect of such rights.

        15. Lost Warrants or Stock Certificates. The Company covenants to the
holder hereof that, upon receipt of evidence reasonably satisfactory to the
Company of the loss, theft, destruction or mutilation of this Warrant or any
stock certificate and, in the case of any such loss, theft or destruction, upon
receipt of an indemnity reasonably satisfactory to the Company, or in the case
of any such mutilation upon surrender and cancellation of such Warrant or stock
certificate, the Company will make and deliver a new Warrant or stock
certificate, of like tenor, in lieu of the lost, stolen, destroyed or mutilated
Warrant or stock certificate.

        16. Descriptive Headings. The descriptive headings of the several
paragraphs of this Warrant are inserted for convenience only and do not
constitute a part of this Warrant. The language in this Warrant shall be
construed as to its fair meaning without regard to which party drafted this
Warrant.

        17. Governing Law. This Warrant shall be construed and enforced in
accordance with, and the rights of the parties shall be governed by, the laws of
the State of California.

        18. Survival of Representations, Warranties and Agreements. All
representations and warranties of the Company and the holder hereof contained
herein shall survive the Date of Grant, the exercise or conversion of this
Warrant (or any part hereof) or the termination or expiration of rights
hereunder. All agreements of the Company and the holder hereof contained herein
shall survive indefinitely until, by their respective terms, they are no longer
operative.

        19. Remedies. In case any one or more of the covenants and agreements
contained in this Warrant shall have been breached, the holders hereof (in the
case of a breach by the Company), or the Company (in the case of a breach by a
holder), may proceed to protect and enforce their or its rights either

                                      -10-
<PAGE>   11

by suit in equity and/or by action at law, including, but not limited to, an
action for damages as a result of any such breach and/or an action for specific
performance of any such covenant or agreement contained in this Warrant.

        20. No Impairment of Rights. The Company will not, by amendment of its
Charter or through any other means, avoid or seek to avoid the observance or
performance of any of the terms of this Warrant, but will at all times in good
faith assist in the carrying out of all such terms and in the taking of all such
action as may be necessary or appropriate in order to protect the rights of the
holder of this Warrant against impairment.

        21. Severability. The invalidity or unenforceability of any provision of
this Warrant in any jurisdiction shall not affect the validity or enforceability
of such provision in any other jurisdiction, or affect any other provision of
this Warrant, which shall remain in full force and effect.

        22. Recovery of Litigation Costs. If any legal action or other
proceeding is brought for the enforcement of this Warrant, or because of an
alleged dispute, breach, default, or misrepresentation in connection with any of
the provisions of this Warrant, the successful or prevailing party or parties
shall be entitled to recover reasonable attorneys' fees and other costs incurred
in that action or proceeding, in addition to any other relief to which it or
they may be entitled.

        23. Entire Agreement; Modification. This Warrant constitutes the entire
agreement between the parties pertaining to the subject matter contained in it
and supersedes all prior and contemporaneous agreements, representations, and
undertakings of the parties, whether oral or written, with respect to such
subject matter.

                                        SIGNAL PHARMACEUTICALS, INC.

                                        By  [SIG]
                                            ------------------------------------

                                        Title V.P. Finance, CFO
                                              ----------------------------------

                                        Address: 5555 Oberlin Drive
                                                 San Diego, California 92121

                                      -11-
<PAGE>   12

                                    EXHIBIT A

                               NOTICE OF EXERCISE

To:  SIGNAL PHARMACEUTICALS, INC.

        1.     The undersigned hereby:

               [ ]    elects to purchase _______ shares of Series C-1 Preferred
                      Stock of SIGNAL PHARMACEUTICALS, INC. pursuant to the
                      terms of the attached Warrant, and tenders herewith
                      payment of the purchase price of such shares in full, or

               [ ]    elects to exercise its net issuance rights pursuant to
                      Section 10.3 of the attached Warrant with respect to
                      Shares of Series C-1 Preferred Stock.

        2.     Please issue a certificate or certificates representing said
shares in the name of the undersigned or in such other name or names as are
specified below:

                         -----------------------------
                                     (Name)

                         -----------------------------

                         -----------------------------
                                    (Address)

        3.     The undersigned represents that the aforesaid shares are being
acquired for the account of the undersigned for investment and not with a view
to, or for resale in connection with, the distribution thereof and that the
undersigned has no present intention of distributing or reselling such shares,
all except as in compliance with applicable securities laws.

                                        ----------------------------------------
                                        (Signature)

----------------
     (Date)

<PAGE>   13

                                   EXHIBIT A-1

                               NOTICE OF EXERCISE

To:  SIGNAL PHARMACEUTICALS, INC. (the "Company")

        1. Contingent upon and effective immediately prior to the closing (the
"Closing") of the Company's public offering contemplated by the Registration
Statement on Form S___, filed _____ __, 19__, the undersigned hereby:

                [ ]     elects to purchase __ shares of Series C-1 Preferred
                        Stock of the Company (or such lesser number of shares as
                        may be sold on behalf of the undersigned at the Closing)
                        pursuant to the terms of the attached Warrant, or

                [ ]     elects to exercise its net issuance rights pursuant to
                        Section 10.3 of the attached Warrant with respect to ___
                        Shares of Series C-1 Preferred Stock.

        2. Please deliver to the custodian for the selling shareholders a stock
certificate representing such ________ shares.

        3. The undersigned has instructed the custodian for the selling
shareholders to deliver to the Company $________ or, if less, the net proceeds
due the undersigned from the sale of shares in the aforesaid public offering. If
such net proceeds are less than the purchase price for such shares, the
undersigned agrees to deliver the difference to the Company prior to the
Closing.

                                        ----------------------------------------
                                        (Signature)

----------------
     (Date)

<PAGE>   14

                                    EXHIBIT B

                                     CHARTER

<PAGE>   15

                                    EXHIBIT C

Information to be provided to the holder prior to the Company's initial public
offering (as described in the Warrant):

        (i) As soon as available but in any event within 30 days after the end
of each monthly accounting period in each fiscal year, unaudited consolidated
statements of operations and consolidated cash flows of the Company and its
subsidiaries for such monthly period, and consolidated balance sheets of the
Company and its subsidiaries as of the end of such monthly period.

        (ii) Prior to the end of each fiscal year, a summary of an annual budget
(approved by the Board of Directors) prepared on a monthly, consolidated basis
for the Company and its subsidiaries for the succeeding fiscal year (displaying
detailed anticipated statements of operations and cash flows and balance
sheets), and promptly upon preparation thereof any other summaries of
significant budgets which the Company prepares and any revisions of such annual
or other budgets.<PAGE>   1

                                                                   EXHIBIT 10.13

                             SECURED PROMISSORY NOTE

$3,000,000                                               Dated: December 2, 1996

        FOR VALUE RECEIVED, the undersigned, SIGNAL PHARMACEUTICALS, INC.
("Borrower"), a California corporation, HEREBY PROMISES TO PAY to the order of
MMC/GATX PARTNERSHIP NO. I, a California general partnership ("Lender") the
principal amount of Three Million Dollars ($3,000,000) or such lesser amount as
shall equal the outstanding principal balance of the Loan made by Lender to
Borrower pursuant to the Loan and Security Agreement referred to below (the
"Loan Agreement"), and to pay all other amounts due with respect to the Loan on
the dates and in the amounts set forth in the Loan Agreement.

        The principal amount of this Note shall be payable in thirty-five (35)
consecutive monthly installments of $83,334.00 per month and a final installment
of $83,310.00 on the last day of each month commencing on June 30, 1997. All
unpaid principal and interest shall, in any event, be payable no later than May
31, 2000.

        Interest on the unpaid principal amount of this Note from the date of
this Note until such principal amount is paid in full shall accrue at the Loan
Rate or, if applicable, the Default Rate. The Loan Rate for this Note is 13.6%
per annum (based on a year of 360 days and actual days elapsed). All accrued
interest shall be payable on the last day of each calendar month, commencing
December 31, 1996.

        Whenever any payment due hereunder shall fall on a day other than a
Business Day, such payment shall be made on the next succeeding Business Day,
and such extension of time shall be included in the computation of interest or
fees, as the case may be.

        Principal, interest and all other amounts due with respect to the Loan,
are payable in lawful money of the United States of America to Lender as
follows: GATX Capital Corporation, P.O. Box 71316, Chicago, Illinois 60694, in
immediately available funds. The Loan made by Lender to Borrower and the
interest rate applicable thereto, and all payments made with respect thereto,
shall be recorded by Lender by Lender on its books. Attached hereto is an
amortization schedule showing the scheduled payments of principal and interest.

        This Note is the Note referred to in, and is entitled to the benefits
of, the Loan and Security Agreement, dated as of November 22, 1996, between
Borrower and Lender. The Loan Agreement, among other things, (a) provides for
the making of a secured Loan by Lender to Borrower in the principal amount first
above mentioned, and (b) contains provisions for acceleration of the maturity
hereof upon the happening of certain stated events.

        Borrower may, at its option, prepay the Loan evidenced by this Note,
either in whole or from time to time in any part of the principal amount thereof
equal to $500,000 or more, at a prepayment price equal to the principal amount
of the Loan so to be prepaid, plus interest accrued thereon through and
including the date of such prepayment, plus the premium set forth in the Loan
Agreement. If the maturity of the Loan is accelerated under the Loan Agreement,
Borrower shall pay to Lender, in addition to principal, interest and all other
amounts due with respect to the Loan, as liquidated damages for loss of Lender's
benefit of the bargain and not as a penalty, an amount equal to the premium
payable if the Loan were prepaid on the date of such acceleration.

        This Note and the obligation of Borrower to repay the unpaid principal
amount of the Loan, interest on the Loan and all other amounts due Lender under
the Loan Agreement is secured under the Loan Agreement.

        Presentment for payment, demand, notice of protest and all other demands
and notices of any kind in connection with the execution, delivery, performance
and enforcement of this Note are hereby waived.

                                      -13-
<PAGE>   2

        Borrower shall pay all reasonable fees and expenses, including, without
limitation, reasonable attorneys' fees and costs, incurred by Lender in the
enforcement or attempt to enforce any of Borrower's obligations hereunder not
performed when due. This Note shall be governed by, and construed and
interpreted in accordance with, the laws of the State of California.

        IN WITNESS WHEREOF, Borrower has caused this Note to be duly executed by
one of its officers thereunto duly authorized on the date hereof.

                                        SIGNAL PHARMACEUTICALS, INC.

                                        By:  /s/ BRAD GORDON
                                             -----------------------------------

                                        Name:    Brad Gordon
                                             -----------------------------------

                                        Title:  V.P. Finance, CFO
                                             -----------------------------------

Source: [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00002-of-00352.parquet"}, [{"source": "alea-institute/alea-institute/kl3m-data-edgar-agreements/train-00002-of-00352.parquet"}]]