<PAGE>

                                 LOAN AGREEMENT

         THIS LOAN AGREEMENT (this "AGREEMENT") is entered into as of 
December 23, 1998 by and between AURORA BIOSCIENCES CORPORATION, a Delaware 
corporation (the "COMPANY"), and THOMAS G. KLOPACK, an individual (the 
"EMPLOYEE").

         WHEREAS, the Employee has agreed to serve as Senior Vice President, 
Strategic Operations, of the Company;

         WHEREAS, the Employee has requested that the Company make a loan to 
the Employee of up to Sixty Thousand Dollars ($60,000); and

         WHEREAS, the Company has agreed to provide the Employee with the 
loan as a portion of the consideration for the Employee's services as an 
employee of the Company.

         NOW, THEREFORE, the parties hereto agree as follows:

         1.    LOAN. The Company shall lend to the Employee an aggregate of 
Sixty Thousand Dollars ($60,000) upon the terms and conditions, and in 
reliance upon the representations and warranties, contained herein (the 
"LOAN").

         2.    METHOD OF FUNDING. The Loan proceeds shall be advanced to the 
Employee by a check payable to the Employee.

         3.    PROMISSORY NOTE. The Loan shall be made pursuant to that 
certain Promissory Note Secured By Deed of Trust dated the date hereof, in 
the stated principal amount of $60,000, in the form attached as EXHIBIT A 
(the "NOTE"). The Employee shall execute the Note concurrently with the 
execution of this Agreement. All repayments of principal with respect to the 
Loan shall be evidenced by notations made by the Company on the Note; 
PROVIDED, HOWEVER, that the failure by the Company to make such notations 
shall not limit or otherwise diminish the obligations of the Employee with 
respect to the Note, including, without limitation, the repayment of 
principal or payments of interest or other amounts, if any, on the Loan.

         4.    INTEREST FREE LOAN. The Company and the Employee agree that, 
so long as Employee is not in default under the Note, the Loan shall not bear 
interest.

         5.    DEED OF TRUST. The Employee hereby agrees to secure the Loan 
by executing a deed of trust granting a second lien on Employee's principal 
residence located at 864 Chelsea Lane, Encinitas, in the County of San Diego, 
California (the "PROPERTY"), in the form attached hereto as EXHIBIT B (the 
"DEED OF TRUST"), which Deed of Trust shall be executed concurrently herewith 
by Employee and Employee's spouse and shall be duly recorded in the official 
records of the County of San Diego, California. Upon such recordation of the 
Deed of Trust, the Employee 

<PAGE>

hereby represents and warrants that, at such time, the Deed of Trust shall 
remain a second lien on the Property, junior only to a Deed of Trust securing 
a note in the stated principal amount $618,300.00 which has been recorded in 
the official records of San Diego County, California. The Employee covenants 
and agrees to promptly execute and deliver all such instruments, agreements 
or other documents as the Company shall reasonably require to obtain the full 
benefits of this Agreement.

         6.    REPAYMENT OF PRINCIPAL; ANNUAL REDUCTION OF PRINCIPAL. The 
outstanding principal amount of the Loan shall become due and payable in a 
single payment immediately upon the earliest to occur of (the "Maturity 
Date"): (i) January 1, 2003; (ii) the sale or other transfer of any interest 
in the Property; or (iii) the business day prior to the six-month anniversary 
of any termination, for any reason, of Employee's employment with the 
Company. Notwithstanding the foregoing, the Company agrees that, on each of 
December 31, 1999, December 31, 2000, December 31, 2001 and December 31, 
2002, the principal amount of the Loan shall be reduced (but not below $0.00) 
by an amount equal to $15,000, PROVIDED that Employee's employment with the 
Company has not been terminated prior to each such date. Employee agrees 
that, as consideration for such reductions in principal, any 
performance-based bonus that Employee might otherwise be eligible to receive 
under the Company's Performance Bonus Plan with respect to each of the 
calendar years 1999, 2000, 2001 and 2002 shall be reduced by fifty percent 
(50%), up to a maximum reduction of $10,000 for each such calendar year.

         7.    PREPAYMENT. The Employee may prepay the unpaid principal in 
whole or in part, without penalty, at any time.

         8.    ITEMIZATION OF DEDUCTIONS. The Employee represents and 
warrants to the Company that he reasonably expects to be entitled to, and 
will, if so entitled, itemize deductions for each year the Loan is 
outstanding.

         9.    NON-TRANSFERABLE. Neither this Agreement nor the rights 
hereunder may be assigned by the Employee without the Company's prior written 
consent.

         10.   GENERAL PROVISIONS.

               (a)   This Agreement shall be governed by the laws of the 
State of California applicable to contracts made and performed in such state, 
without regard to principles of conflicts of laws.

               (b)   This Agreement and its Exhibits constitute the entire 
agreement between the Employee and the Company, and is the complete, final, 
and exclusive embodiment of their agreement with regard to this subject 
matter. The Employee and the Company each acknowledge

and represent that this Agreement is entered into without reliance on any 
promise or representation other than those expressly contained herein and 
that this Agreement cannot be modified except in a writing signed by both 
parties.

<PAGE>

               (c)   Except as otherwise specified herein, any notice, demand 
or request required or permitted to be given by either the Company or the 
Employee pursuant to the terms of this Agreement shall be in writing and 
shall be deemed given when delivered personally, three days after being 
deposited in the U.S. Mail, registered mail, return receipt requested, 
postage prepaid, or one business day after delivery to an overnight carrier 
service and addressed to the Company at its then current principal office and 
to the Employee at the address listed for him on the Company's payroll.

               (d)   Either party's failure to enforce any provision or 
provisions of this Agreement shall not in any way be construed as a waiver of 
any such provision or provisions, nor prevent that party thereafter from 
enforcing each and every other provision of this Agreement. The rights 
granted both parties herein are cumulative and shall not constitute a waiver 
of either party's right to assert all other legal remedies available to it 
under the circumstances.

               (e)   the Employee agrees upon request to execute any further 
documents or instruments necessary or desirable to carry out the purpose or 
intent of this Agreement.

               (f)   In the event of any litigation concerning this 
Agreement, the prevailing party shall be entitled to a reasonable sum for 
attorneys' fees, costs, and litigation expenses, whether or not such action 
is prosecuted to judgment. "Prevailing Party" includes, without limitation, a 
party who agrees to dismiss an action upon payment by the other party of sums 
allegedly due or performance of the covenants allegedly breached, or who 
obtains substantially the relief sought by that party. In the event that the 
Company is the Prevailing Party, the Company shall also be entitled to 
reasonable costs associated with the collection of the Loan.

               (g)   This Agreement may be executed in counterparts, each of 
which shall be an original, but all of which together shall constitute one 
instrument.

         IN WITNESS WHEREOF, the parties have duly executed this Agreement as of
the day and year first set forth above.

AURORA BIOSCIENCES CORPORATION

By:      /s/ TIMOTHY J. RINK
         ---------------------------------------------
         Timothy J. Rink, M.D., Sc.D.
         Chairman, Chief Executive Officer & President

/s/THOMAS G. KLOPACK
---------------------------------------
THOMAS G. KLOPACK

<PAGE>

                                    EXHIBIT A

                                 PROMISSORY NOTE

<PAGE>

         DO NOT DESTROY THIS NOTE: WHEN PAID, THIS NOTE AND THE DEED OF
              TRUST SECURING IT MUST BE SURRENDERED TO TRUSTEE FOR
                 CANCELLATION BEFORE RECONVEYANCE WILL BE MADE.

                             PROMISSORY NOTE SECURED
                             BY SECOND DEED OF TRUST

                                                               December 23, 1998

         FOR VALUE RECEIVED, THOMAS G. KLOPACK, an individual ("Maker"), 
promises to pay AURORA BIOSCIENCES CORPORATION, A DELAWARE CORPORATION 
("Holder") at 11010 Torreyana Road, San Diego, California, 92121, or such 
other place as Holder may from time to time designate, in lawful money of the 
United States, the principal sum SIXTY THOUSAND DOLLARS AND NO CENTS 
($60,000.00), together with any interest or other amounts due thereon (the 
"Loan"), payable in the manner set forth below and in accordance with the 
terms and conditions of that certain Loan Agreement of even date herewith 
between Holder and Maker (as such may from time to time be amended, modified, 
restated or supplemented, the "Loan Agreement"):

         11.   PRINCIPAL REPAYMENT/MATURITY DATE. Principal shall be due and 
payable in full on the Maturity Date, which date shall be determined pursuant 
to the Loan Agreement. Other repayments of principal shall be due and payable 
in accordance with the Loan Agreement.

         12.   PREPAYMENT. This Note may be prepaid in whole or in part, at 
any time, without penalty or premium, on any date prior to the Maturity Date.

         13.   PAYMENTS/ADMINISTRATION. Any amounts payable hereunder shall 
be due and payable without set-off, deduction, or counterclaim, except as 
otherwise provided herein. The Loan, and all repayments and reductions of 
principal and interest, if any, shall be evidenced by notations made by 
Holder in its books and records regarding the date and amount of each payment 
or reduction of principal and interest made by Maker with respect thereto; 
PROVIDED, HOWEVER, that the failure by Holder to make such notations shall 
not limit or otherwise diminish the obligations of Maker with respect to the 
repayments or reductions of principal or payments of interest, if any, on the 
Loan. The aggregate unpaid amount of the Loan set forth on the books and 
records of Holder shall be presumptive evidence of the principal amount owing 
an unpaid hereunder.

         14.   SECURITY. This Note is secured by a second deed of trust of 
even date herewith from Maker and Adrienne Klopack ("Spouse"), as trustor, 
naming Holder as beneficiary (the "Deed of Trust"), granting a security 
interest in certain real property located in the City of Encinitas, County of 
San Diego, California, as more particularly described therein (the 
"Property"). Maker hereby represents and warrants that, after giving effect 
to Maker's purchase of the Property, Maker and Spouse will be the sole and 
lawful fee owner of the Property.

<PAGE>

         15.   DEFAULT AND REMEDIES.

               (a)   DEFAULT. Maker will be in default under this Note upon 
the occurrence of any one or more of the following events: (i) the failure of 
Maker to make any payment required hereunder when due, (ii) the breach by 
Maker of any other covenant or agreement under this Note, (iii) the default 
by Maker of its obligations under the Deed of Trust, the Loan Agreement, or 
any other instrument evidencing or securing this Note, (iv) the default by 
Maker of its obligations under any mortgage, deed of trust, encumbrance or 
lien respecting the Property, which encumbrance is senior to the Deed of 
Trust, (v) the appointment of a receiver for any part of the property of, or 
an assignment for the benefit of creditors by, or the commencement of any 
proceedings under any bankruptcy or insolvency laws by or against any maker, 
endorser or guarantor, or (vi) the transfer, directly or indirectly, of all 
or any part of any interest in the Property, whether by sale, lease, 
assignment, mortgage or otherwise, voluntarily or involuntarily.

               (b)   REMEDIES. Upon Maker's default, Holder may, with notice 
to Maker, declare the entire principal sum and any amounts due thereon 
immediately due and payable and exercise any and all of the remedies provided 
under the Deed of Trust or at law or in equity.

               (c)   DEFAULT INTEREST. If any amount payable hereunder shall 
not be paid within forty-five (45) days after the Maturity Date, at the 
option of Holder, the unpaid principal balance shall immediately begin to 
accrue interest at a rate of 8.0%, and Holder shall have all remedies 
available to it by law as a creditor hereunder.

         16.   WAIVERS. Maker, and any endorsers or guarantors hereof, 
severally waive diligence, presentment, protest and demand and also notice of 
protest, demand, dishonor, acceleration, intent to accelerate, and nonpayment 
of this Note, and expressly agree that this Note, or any payment hereunder, 
may be extended from time to time without notice, and consent to the 
acceptance of further security or the release of any security for this Note, 
all without in any way affecting the liability of Maker or any endorsers or 
guarantors hereof. No extension of time for the payment of this Note, or any 
installment hereof, agreed to by Holder with any person now or hereafter 
liable for the payment of this Note, shall affect the original liability of 
Maker under this Note, even if Maker is not a party to such agreement.

         17.   MAXIMUM LEGAL RATE OF INTEREST. All agreements between Maker 
and Holder, whether now existing or hereafter arising, are hereby limited so 
that in no event shall the interest charged hereunder or agreed to be paid to 
Holder exceed the maximum amount permissible under applicable law. Holder 
shall be entitled to amortize, prorate and spread throughout the full term of 
this Note all interest paid or payable so that the interest paid does not 
exceed the maximum amount permitted by law. If Holder ever receives interest 
or anything deemed interest in excess of the maximum lawful amount, an amount 
equal to the excessive interest shall be applied to the reduction of the 
principal, and if it exceeds the unpaid balance of principal hereof, such 
excess shall be refunded to Maker. If interest otherwise payable to Holder 
would exceed the maximum lawful amount, the interest payable shall be reduced 
to the maximum amount permitted under applicable law. This paragraph shall 
control all agreements between Maker and Holder in connection with the 
indebtedness evidenced hereby.

<PAGE>

         18.   NOTICE. All notices or other communications required or given 
hereunder shall be in writing and shall be deemed given when delivered 
personally, three days after being deposited in the U.S. Mail, registered 
mail, return receipt requested, postage prepaid, or one business day after 
delivery to an overnight carrier service and addressed to Holder at its then 
current principal office and to Maker at the address listed for him in the 
Company's payroll records.

         19.   MISCELLANEOUS.

               (a)   Maker shall pay all costs, including, without 
limitation, reasonable attorneys' fees incurred by Holder in collecting the 
sums due hereunder or in connection with the release of any security for this 
Note.

               (b)   This Note may be modified only by a written agreement 
executed by Maker and Holder.

               (c)   This Note shall be governed by California law without 
regard to principals of conflicts of laws.

               (d)   Time is of the essence with respect to all matters set 
forth in this Note.

               (e)   The terms of this Note shall inure to the benefit of and 
bind Maker and Holder and their respective heirs, legal representatives and 
successors and assigns.

               (f)   If this Note is destroyed, lost or stolen, Maker will 
deliver a new note to Holder on the same terms and conditions as this Note 
with a notation of the unpaid principal in substitution of the prior Note. 
Holder shall furnish to Maker reasonable evidence that the Note was 
destroyed, lost or stolen and any security or indemnity that may be 
reasonably required by Maker in connection with the replacement of this Note.

               (g)   If any provision of this Note shall be held to be 
invalid or unenforceable, such determination shall not affect the remaining 
provisions of this Note.

               (h)   If this Note is now, or hereinafter shall be, signed by 
more than one party or person, it shall be the joint and several obligation 
of such parties or persons and shall be binding upon such parties and upon 
their respective successors and assigns.

               (i)   In the event an action is commenced to interpret or 
enforce this Note or to collect any sums due hereunder, the prevailing party 
shall be entitled to receive from the other party, attorneys' fees and costs 
as determined by the court in which such action is pending.

<PAGE>

         IN WITNESS WHEREOF, Maker has executed this Note as of the date and 
year first above written.

                                           MAKER:

                                           /s/ THOMAS G. KLOPACK
                                           -----------------------------------
                                           THOMAS G. KLOPACK