Document:

exv4w11

Exhibit 4.11

Loan and Security Agreement

This Loan and Security Agreement no. 1452 (this “Agreement”) is entered into as of January
27, 2010, by and between Kior, Inc., a Delaware corporation (“Borrower”) and
Lighthouse Capital Partners VI, L.P. as “Agent” for the lenders identified on Schedule A
hereto (such lenders, together with their respective successors and assigns are referred to herein
each individually as a “Lender” and collectively as “Lenders”), and the Lenders. This Agreement
sets forth the terms and conditions upon which Lenders will lend and Borrower will repay money. In
consideration of the mutual covenants herein contained, the parties agree as follows:

1. Definitions and Construction

1.1 Definitions. Initially capitalized terms used and not otherwise defined herein are defined in
the California Uniform Commercial Code (“UCC”).

“ACH” means the Automated Clearing House electronic funds transfer system.

“Advance” means a Loan advanced by Lender to Borrower hereunder.

“Agent” means Lighthouse Capital Partners VI, L.P. or any successor Agent appointed by the Lenders.

“Basic Rate” a per annum rate of interest equal to (i) for Advances funded under Tranche 1, 12% and
(ii) for Advances funded under Tranche 2, 14% during the Interest Only Period and 12% on and after
the Loan Commencement Date.

“Borrower’s Books” means all of Borrower’s books and records, including records concerning
Collateral, Borrower’s assets, liabilities, business operations or financial condition, on any
media, and the equipment containing such information,

“Collateral” means: (i) all property in which Agent on behalf of Lenders now has or hereafter
obtains a security interest under this Agreement or which is listed on UCC-I naming Borrower as
Debtor in any capacity and Agent, Lenders or an affiliate of Lenders as Secured Party including
Exhibit A attached hereto; and (ii) all products and proceeds of the foregoing, including proceeds
of insurance and proceeds of proceeds. Notwithstanding the foregoing, Collateral shall not include
(i) any Eligible Equipment financed under (and as defined under) the Lighthouse Equipment Loan, but
only for so long as the Obligations under the Lighthouse Equipment Loan are outstanding or (ii)
property secured pursuant to clause (v) of the definition of Permitted Liens.

“Commitment” means $10,000,000, available in 2 tranches. Tranche 1, in the amount of $7,000,000
(“Tranche I”) shall be available immediately upon the closing of this Agreement; Tranche 2, in the
amount of $3,000,000 (“Tranche 2”) shall be available upon Borrower reaching any of the following
milestones: (i) formal approval of a United Stated Department of Energy or United States Department
of Agriculture (or a combination of both) commercialization grant totaling at least $20,000,000;
(ii) proof reasonably acceptable to Agent of Demonstration Facility’s full operational capability
of at least 10 barrels per day of bio-oil within a 24 hour operation period; (iii) close of a
preferred stock equity financing led by a new outside investor of at least $30,000,000 (which
amount may include conversion of a $15,000,000 bridge facility provide by Khosla Ventures); or (iv)
finalization of a strategic partnership agreement with a large, multinational oil company deemed
acceptable to Agent in its reasonable discretion. Each Lender shall be responsible for no more than
the percentage amount of each Advance, as reflected on Schedule A hereto and shall have no
liability for the Commitment to make Advances of any other Lender.

“Commitment Fee” means $15,000.

“Commitment Termination Date” means the earliest to occur of (i) (a) for Tranche l, January 31,
2010; and (b) for Tranche 2, July 31, 2010; (ii) any Event of Default or, during the pendency of a
Default unless and until such time as such Default is cured to Agent’s sole reasonable
satisfaction; (iii) the date on which Mr. Fred Cannon, Borrower’s President or at least one
representative of Khosla Ventures II, LP or its affiliated finds ceases to serve as a member of
Borrower’s Board of Directors; or (iv) the date on which Borrower ceases to be in the business of
developing and manufacturing biofuels.

“Control Agreement” means an agreement substantially in the form of Exhibit I or otherwise
acceptable to Agent.

“Default” means any event that with the passing of time or the giving of notice or both would
become an Event of Default.

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“Default” Rate” means the lesser of 18% per annum or the highest rate permitted by applicable law.

“Demonstration Facility” means Borrower’s facility located at 13001 Bay Park Road, Pasadena, TX
77507.

“Disclosure Schedule” means the schedule attached as Schedule I hereto.

“Event of Default” is defined in Section 8.

“Funding Date” means any date on which an Advance is made to or on account of Borrower hereunder.

“Incumbency Certificate” means the document in the form of Exhibit E.

“Indebtedness” means (i) all indebtedness for borrowed money or the deferred purchase of property
or services (other than trade payables), (ii) all obligations evidenced by notes, bonds, debentures
or similar instruments, (iii) all capital lease obligations, and (iv) all contingent obligations,
including guaranties and obligations of reimbursement or respecting letters of credit.

“Interest Only Period” means, for Advances funded under Tranche 2, the period commencing on the
Funding Date of such Advance and continuing through the day immediately preceding the Loan
Commencement Date.

“Investment” means any beneficial ownership of (including stock, partnership or limited liability
company interest or other securities) any entity, or any loan, advance or capital contribution of
any entity or person.

“Kior BV” means Kior BV, a wholly-owned subsidiary of Borrower organized under the laws of The
Netherlands.

“Lenders’ Expenses” means all reasonable costs or expenses (including reasonable attorneys’ fees
and expenses) incurred in connection with the preparation, negotiation, modification,
administration, or enforcement of the Loan or Loan Documents, or the exercise or preservation of
any rights or remedies by Agent or Lenders, whether or not suit is brought. Agent and Lenders will
apply deposits received before the date hereof, if any, towards Lender’s Expenses.

“Lien” means any lien, security interest, pledge, bailment, lease, mortgage, hypothecation,
conditional sales and title retention agreement, charge, claim, or other encumbrance.

“Lighthouse Equipment Loan” means that certain Loan and Security Agreement No. 1451 dated December
30, 2008 by and between Lighthouse Capital Partners VI, L.P. and Borrower.

“Loan” means all of the Advances, however evidenced, and all other amounts due or to become due
hereunder.

“Loan Commencement Date” means August 1, 2010,

“Loan Documents” means, collectively, this Agreement, the Warrant, the Notes, and all other
documents, instruments and agreements entered into between Borrower and Lenders in connection with
the Loan, all as amended or extended from time to time.

“Material Adverse Effect” means a material adverse effect on (i) the financial condition of
Borrower and its Subsidiaries taken as a whole or (ii) the validity or enforceability of the Loan
Documents or the rights and remedies of the Lenders thereunder or with respect to the Collateral.

“Negative Pledge Agreement” means an agreement in the form of Exhibit H.

“Note” means a Secured Promissory Note in the form of Exhibit B.

“Notice of Borrowing” means the form attached as Exhibit D.

“Obligations” means all Loans, debt, principal, interest, fees, charges, Lender’s Expenses and
other amounts, obligations, covenants, and duties owing by Borrower to Agent or Lenders of any kind
or description (pursuant to the Loan Documents (with the exception of the Warrant), and whether or
not for the payment of money), whether direct or indirect, absolute or contingent, due or
to become due, now existing or hereafter arising, and including any of the same obtained by Agent
or Lenders by assignment or otherwise, and all amounts Borrower is required to pay or reimburse by
the Loan Documents, by law, or otherwise.

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“Permitted Indebtedness” means: (i) the Loan; (ii) unsecured trade debt incurred in the ordinary
course of Borrower’s or any Subsidiary’s business; (iii) Indebtedness secured by clauses (ii), (v),
and (vi) of Permitted Liens; (iv) Indebtedness of the Borrower or any Subsidiary to the Borrower or
any Subsidiary in the ordinary course of business; (v) Indebtedness set forth on the Disclosure
Schedule as of the date of this Agreement; (vii) Subordinated Indebtedness; and (vii) extensions,
refinancing, modifications, amendments and restatements of any items of Permitted Indebtedness
above, provided that the principal amount thereof is not increased or the terms thereof are not
modified to impose more burdensome terms upon Borrower or a Subsidiary, as the case may be.

“Permitted Investments” means (i) Investments existing as of the date hereof and disclosed oil the
Disclosure Schedule; (ii) (a) marketable direct obligations issued or unconditionally guaranteed by
the United States of America or any agency or any State thereof maturing within I year from the
date of acquisition thereof, (b) commercial paper maturing no more than one year from the date of
creation thereof and currently having a rating of at least A-2 or P-2 from either Standard & Poor’s
Corporation or Moody’s Investors Service, (c) certificates of deposit maturing no more than I year
from the date of investment therein, and (d) money market accounts; (iii) Investments made pursuant
to an investment policy approved by the Board of Directors that is designed to maintain liquidity
and preserve capital with respect to Borrower’s excess cash; (iv) Investments not to exceed.
$100,000 in the aggregate in any fiscal year consisting of (a) travel advances and employee
relocation loans and other employee loans and advances in the ordinary course of business and (b)
loans to employees, officers and directors relating to the purchase of equity securities of
Borrower pursuant to employee stock purchase plan agreements approved by Borrower’s Board of
Directors; (v) Investments (including debt obligations) received in connection with the bankruptcy
or reorganization of customers or suppliers and in settlement of delinquent obligations of, and
other disputes with, customers or suppliers arising in the ordinary course of Borrower’s business;
(vi) Investments consisting of notes receivable of, or prepaid royalties and other credit
extensions, to customers and suppliers who are not affiliates, in the ordinary course of business;
and (vii) deposit accounts maintained by Borrower in the ordinary course of business; and (viii)
Investments by Borrower into Subsidiary or by a Subsidiary into another Subsidiary to fund such
Subsidiary’s ordinary course operations.

“Permitted Liens” means: (i) Liens in favor of Lender; (ii) Liens disclosed in the Disclosure
Schedule; (iii) Liens for taxes, fees, assessments or other governmental charges or levies not
delinquent or being contested in good faith by appropriate proceedings, that do not jeopardize
Lender’s interest in any Collateral; (iv) Liens to secure payment of worker’s compensation,
employment insurance, old age pensions or other social security obligations of Borrower or any
Subsidiary on which Borrower or any Subsidiary is current and are in the ordinary course of its
business; provided none of the same diminish or impair Lender’s rights and remedies respecting the
Collateral; (v) Liens on any property held or acquired by Borrower or any Subsidiary in the
ordinary course of business securing Indebtedness incurred or assumed for the purpose of financing
all or any part of the cost of acquiring such property, provided such Lien attaches solely to the
property acquired with such Indebtedness and that the principal amount of such Indebtedness does
not exceed 100% of the cost of such property, in an aggregate amount not to exceed $1,000,000 and
provided further such Indebtedness is on commercially reasonable terms; (vi) licenses or
sublicenses of intellectual property granted in the ordinary course of business; (vii) banker’s
Liens, rights of setoff and similar Liens incurred on deposit and securities accounts of such
entities for fees due on such accounts incurred in the ordinary course of business; (viii)
carriers’, warehousemen’s, mechanics’, materialmen’s, repairmen’s or other like Liens arising in
the ordinary course of business which are not delinquent or remain payable without penalty or which
are being contested in good faith and by appropriate proceedings for which adequate reserves are
kept; (ix) Liens in favor of customs and revenue authorities which secure payment of customs duties
in connection with the importation of goods; and (x) Liens incurred in the extension, renewal or
refinancing of the Indebtedness secured by Liens described above but any extension, renewal or
replacement Lien must be limited to the property originally encumbered by the existing Lien and the
principal amount of any Indebtedness associated therewith may not increase.

“Regulated Substance” means any substance, material or waste the use, generation, handling,
storage, treatment or disposal of which is regulated by any local or state government authority,
including any of the same designated by any authority as hazardous, genetic, cloning, fetal, or
embryonic.

“Responsible Officer” means the President, Chief Financial Officer/Treasurer and Secretary of
Borrower and each person as authorized by the board of directors of Borrower as set forth on the
Incumbency Certificate.

“Subordinated Indebtedness” means Indebtedness in an amount not to exceed $5,000,000 that is
subordinated in both security and right of payment to the Obligations on terms and conditions
satisfactory to Lenders as evidenced by a subordination agreement between Lenders and the
provider(s) of such Subordinated Indebtedness.

“Subsidiary” means any corporation of which a majority of the outstanding capital stock entitled to
vote for the election of directors (otherwise than as the result of a default) is owned by Borrower
directly or indirectly through Subsidiaries.

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“Term” means the period from and after the date hereof until the full, final and indefeasible
payment and performance of all Obligations,

“Tranche 2 Warrants” means the Warrant in favor of each of the Lenders and its affiliates to
purchase securities of Borrower substantially in the form of Exhibit C-1 issued in conjunction with
the availability of Tranche 2 of the Commitment,

“Warrant” or “Warrants” means the Warrant in favor of each of the Lenders and its affiliates to
purchase securities of Borrower substantially in the form of Exhibit C and the Tranche 2 Warrants.

1.2 Interpretation. References to “Articles,” “Sections,” “Exhibits,” and “Schedules” are to
articles, sections, exhibits and schedules herein and hereto unless otherwise indicated. “Hereof,”
“herein” and “hereunder” refer to this Agreement as a whole, “Including” is not limiting. All
accounting and financial computations shall be computed in accordance with generally accepted
accounting principles consistently applied (“GAAP”). “Or” is not necessarily exclusive. All
interest computation shall be based on 360-day year and actual days elapsed prior to the Loan
Commencement Date and on a 360-day year and 30 day month on and after the Loan Commencement Date.

2. The Loans

2.1 Commitment. Subject to the terms hereof, Lenders will make Advances to Borrower up to the
principal amount of their respective shares of the Commitment, oil before the Commitment
Termination Date. Notwithstanding anything in the Loan Documents to the contrary, Lenders’
obligation to make any Advances or to lend the undisbursed portion of the Commitment shall
terminate on the Commitment Termination Date. Repaid principal of the Advances may not be
re-borrowed.

2.2 The Advances. A Note setting forth the specific terms of repayment will evidence each Advance.
No Advance will be made for less than $500,000, unless less than $500,000 remains available under
the Commitment for borrowing. Absence of a Note evidencing any portion of the Loan shall not impair
Borrower’s obligation to repay it to Lenders under the terms outlined in Exhibit B for the
applicable Note for the amount of each Advance. Each Lender will receive a Note from Borrower
evidencing the Advances funded by such Lender at the time of each such Advance (if any).

2.3 Terms of Payment, Repayment.

     (a) Repayment. Borrower shall repay the principal and pay interest on each Advance on the terms set
forth in the applicable Note. Amounts not paid when due hereunder or under the Note shall bear
interest at the Default Rate. If a court of competent jurisdiction determines that a Lender has
received payments that, if interest, would exceed the maximum lawfully permitted, such Lender will
instead apply such money to fees and expenses and then to early prepayment of principal (without
any Prepayment Fee (as defined in the Note).

     (b) ACH. All payments due to Lenders must be, at each Lender’s option, paid to Lender in cash or
through ACH. Borrower shall execute and deliver the ACH Authorization Form for each Lender
substantially in the form of Exhibit G. If the ACH payment arrangement is terminated for any reason
with respect to any Lender, Borrower shall make all payments due to such Lender at such Lender’s
address specified in Section 11.

     (c) Default Rate. While an Event of Default has occurred and is continuing, interest on the Loan shall be increased
to the Default Rate. Any Lender’s failure to charge or accrue interest at the Default Rate during
the existence of a Default shall not be deemed a waiver by any Lender of any right or claim
thereto.

     (d) Date. Whenever any payment due under the Loan Documents is due 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.

2.4 Fees. Borrower shall pay to Lenders the following:

     (a) Commitment Fee. The Commitment Fee, which has been previously paid by Borrower to Agent, and
shall be applied by Agent to Lenders’ Expenses and other Obligations.

     (b) Late Fee. On demand, a late charge on any sums due hereunder that are not paid when due, in an
amount equal to 2% of the past due amount, payable on demand.

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     (c) Lender’s Expenses. When requested, all Lenders’ Expenses. Lenders’ Expenses not paid when due
shall bear interest as principal at the Default Rate.

3. Conditions of Advances; Procedure for Requesting Advances

3.1 Conditions Precedent to any and all Advances. The obligation of Lenders to make any Advances is
subject to each and every of the following conditions precedent in form and substance satisfactory
to Agent in its sole discretion: (i) this Agreement, a Note evidencing the Advance, the Warrants
(with respect to Tranche 2, the Tranche 2 Warrants), and all other UCC financing statements, and
other documents required or as specified herein have been duly authorized, executed and delivered
to the Agent and/or the Lenders; (ii) no Default or Event of Default has occurred and is
continuing, (iii) delivery of a Notice of Borrowing to Agent with respect to the proposed Advance;
(iv) Lenders’ security interests in the Collateral are valid and first priority, except for
Permitted Liens; and (v) all such other items as Agent may reasonably deem necessary or appropriate
have been delivered or satisfied. The extension of an Advance prior to the receipt by Lenders of
any of the foregoing shall not constitute a waiver by any of the Lenders of Borrower’s obligation
to deliver such item. In addition to the foregoing, it shall be a condition to the funding of any
Advances under Tranche 2, that Borrower shall issue Lenders the Tranche 2 Warrants.

3.2 Procedure for Making Advances. For any Advance, Borrower shall provide Agent an irrevocable
Notice of Borrowing at least 10 business days prior to the desired Funding Date and Lenders shall
only be required to make Advances hereunder based upon written requests which comply with the terms
and exhibits of this Loan Agreement (as the same may be amended from time to time), and which are
submitted and signed by a Responsible Officer. Borrower shall execute and deliver to Lenders a Note
and such other documents and instruments as Lenders may reasonably require for each Advance made.

4. Creation of Security Interest

4.1 Grant of Security Interest. Borrower grants to Agent on behalf of all Lenders a valid, first priority (subject to Permitted
Liens), continuing security interest in all present and future Collateral in order to secure
prompt, full, faithful and timely payment and performance of all Obligations.

4.2 Inspections. Agent shall have the right upon reasonable prior notice to inspect Borrower’s
Books, including computer files, and to make copies, and to test, inspect and appraise the
Collateral, in order to verify any matter relating to Borrower or the Collateral. Lenders may
accompany Agent on such inspections.

4.3 Authorization to File Financing Statements. Borrower irrevocably authorizes Agent on behalf of
all Lenders at any time and from time to time to file in any jurisdiction any financing statements
and amendments that: (i) name Collateral as collateral thereunder, regardless of whether any
particular Collateral falls within the scope of the UCC; (ii) contain any other information
required by the UCC for sufficiency or filing office acceptance, including organization
identification numbers; and (iii) contain such language as Lender determines helpful in protecting
or preserving rights against third parties. Borrower ratifies any such filings made prior to the
date hereof.

5. Representations and Warranties

Borrower represents and warrants as follows:

5.1 Due Organization and Qualification. Borrower is a corporation duly formed, existing and in good
standing under the laws of its state of incorporation and qualified and licensed to do business in,
and is in good standing in, any state in which the conduct of its business or its ownership of
property requires that it be so qualified or in which the Collateral is located, except states
other than Texas and Delaware where non-compliance would not reasonably be expected to have a
Material Adverse Effect on Borrower or any of the Collateral.

5.2 Authority. Borrower has all corporate power and authority, and has taken all actions, and has
obtained all third party consents necessary to execute, deliver, and perform the Loan Documents.

5.3 Disclosure Schedule. All information on the Disclosure Schedule is true, correct and complete.

5.4 Authorization; Enforceability. The execution and delivery hereof, the granting of the security
interest in the Collateral, the incurring of the Obligations, the execution and delivery of all
Loan Documents and the consummation of the transactions herein and therein contemplated have been
duly authorized by all necessary action by Borrower. The Loan Documents constitute legal,

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valid and
binding obligations of Borrower, enforceable in accordance with their terms, except as
enforceability may be limited by bankruptcy or similar laws relating to enforcement of creditors`
rights generally.

5.5 Name and Location. Borrower has not done business under any name other than that specified on
the signature page hereof or as set forth on the Disclosure Schedule. Except as provided in any
written notice from Borrower to Lender, (i) the chief executive office, principal place of
business, and the place where Borrower maintains its records concerning the Collateral is set forth
in Section 11 and (ii) the Collateral is presently located at the address(es) set forth in Section
11 and on the Disclosure Schedule. Borrower has no subsidiaries except as set forth on the
Disclosure Schedule.

5.6 Litigation. All actions or proceedings pending or, to Borrower’s knowledge, threatened by or
against Borrower before any court or administrative agency are set forth on the Disclosure
Schedule.

5.7 Financial Statements. All financial statements of the Borrower and its consolidated
Subsidiaries delivered by Borrower to Lender fairly present in all material respects the financial
condition of the Borrower and its consolidated Subsidiaries, taken as a whole. All schedules
respecting Collateral that have been or may hereafter be delivered by Borrower to Lender are true,
complete and correct in all material respects for the periods indicated.

5.8 Solvency. Borrower is solvent and able to pay its debts (including trade debts) as they come
due.

5.9 Taxes. Borrower has filed all required tax returns, and has paid all taxes it owes other than
where the failure to comply would not reasonably be expected to have a Material Adverse Effect.

5.10 Rights; Title to Assets. Borrower possesses and owns all necessary assets, rights, trademarks,
trade names, copyrights, patents, patent rights, franchises and licenses which it needs to conduct
its business as now operated or proposed to be operated. Borrower has good title to its assets,
free and clear of any Liens, except for Permitted Liens.

5.11 Full Disclosure. No written representation, warranty or other statement made by Borrower in
any Loan Document, certificate or statement furnished to Lender contains any untrue statement of a
material fact or omits to state a material fact necessary in order to make the statements contained
in such certificates or statements not misleading.

5.12 Regulated Substances. Borrower complies with all laws respecting Regulated Substances in all
material respects.

5.13 Reaffirmation. Each Notice of Borrowing will constitute (i) a warranty and representation in
favor of Agent and Lenders that there does not exist any Default and (ii) a reaffirmation as of the
date thereof of all of the representations and warranties contained in this Agreement and the Loan
Documents.

5.14 Auction Rate Securities. The Borrower (i) owns no auction rate securities or similar financial
instruments directly or indirectly in any brokerage, securities account or other account created by
or for the benefit of the Borrower; and (ii) has not created any standing or discretionary purchase
order or directive with any brokerage account or broker service to purchase auction rate securities
or similar financial instruments on behalf of the Borrower.

5.15 Kior BV. Borrower represents and warrants that Kior BV (i) has no property, assets, operating
contracts or business operations, except for any assets that are immaterial to the business of
Borrower, and is not bound by and is not a party to, any contacts that are material to the Borrower
(ii) has no employees (iii) has not issued any stock certificates and (iv) has no material
liabilities on its balance sheet for which it or Borrower is responsible. Neither Borrower nor Kior
BV has granted a security interest in any of the shares of capital stock of Kior BV. Kior BV is a
wholly subsidiary of Borrower.

6. Affirmative Covenants

Borrower covenants and agrees that it shall do all of the following:

6.1 Good Standing and Compliance. Borrower shall maintain all governmental licenses, rights and
agreements necessary for its operations or business and comply with all statutes, laws, ordinances
and government rules and regulations to which it is subject, except where the failure to do so
would not reasonably be expected to result in a Material Adverse Effect.

6.2 Financial Statements, Reports, Certificates. Borrower shall deliver to Agent: (i) as soon as
prepared, and no later than 30 days after the end of each calendar month, a balance sheet, income
statement and cash flow statement covering Borrower’s operations during such period; (ii) as soon
as prepared, but no later than 120 days after the end of the fiscal year or such other time

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period
as approved by Borrower’s Board of Directors, (x) audited financial statements prepared in
accordance with GAAP, together with an opinion that such financial statements fairly present
Borrower’s financial condition by an independent public accounting firm reasonably acceptable to
Agent, or (y) in the absence of an initial audit, financial statements for such fiscal year
prepared in accordance with GAAP and certified by a Responsible Officer or approved by the Board of
Directors of Borrower; (iii) immediately upon notice thereof, a report of any legal or
administrative action pending or threatened against Borrower which is likely to result in liability
to Borrower in excess of $200,000; and (iv) such other financial information that is periodically
delivered to Borrower’s preferred stockholders or as Lender may reasonably request from time to
time. Financial statements delivered pursuant to subsections (i) and (ii) above shall be
accompanied by a certificate signed by a Responsible Officer (each an “Officers Certificate”) in
the form of Exhibit F.

6.3 Notice of Defaults. Promptly following any Default or Event of Default, deliver an Officer’s
Certificate to Agent setting forth the facts relating to or giving rise thereto, and the Borrower’s
proposed action with respect thereto.

6.4 Use; Maintenance. Borrower, at its expense, shall (i) maintain the Collateral in good
condition, reasonable wear and tear excepted, and will comply in all material respects with all
laws, rules and regulations regarding use and operation of the Collateral and (ii) repair or
replace any lost or damaged Collateral.

6.5 Insurance. Borrower, at its own expense, shall maintain insurance in amounts and coverages
reasonably satisfactory to Lender. Each insurance policy shall: (i) name Agent on behalf of all
Lenders as loss payee or additional insured, as appropriate, (ii) provide for insurer’s waiver of
its right of subrogation against Lenders and Borrower, (iii) provide that such insurance shall not
be invalidated by any action of, or breach of warranty by, Borrower and waive set-off, counterclaim
or offset against Lenders, (iv) be primary without a right of contribution of Lenders’ insurance,
if any, or any obligation on part of Lenders to pay premiums of Borrower, and (v) require the
insurer to give Agent at least 30 days prior written notice of cancellation, unless such
cancellation is on account of non-payment in which case 10 days prior written notice shall be
sufficient. Borrower shall furnish all certificates of insurance required by Agent.

6.6 Loss Proceeds. So long as no Event of Default has occurred and is continuing, any proceeds of
insurance on or condemnation of Collateral shall, at Borrower’s election and so long as Lenders’
security interest in such proceeds remains first priority, be used either to repair or replace such
Collateral or otherwise applied to the purchase or acquisition of property useful to Borrower’s
business.

6.7 Taxes. Borrower will file all required tax returns, and will pay all taxes it owes other than
where the failure to comply would not reasonably be expected to have a Material Adverse Effect.

6.8 Regulated Substances. Borrower will comply with all laws respecting Regulated Substances and
shall not incur any penalties with regards to such Regulated Substances in an amount not to exceed
$200,000 of remedial cost, which penalty has not been dismissed or paid within 30 days.

6.9 Further Assurances. At any time and from time to time, Borrower shall execute and deliver such
further instruments and take such further action as Agent may reasonably request to effect the
intent and purposes hereof, to perfect and continue perfected and of first priority Lenders”
security interests in the Collateral, and to effect and maintain ACH payment arrangements with each
of the Lenders.

6.10 Dissolution of Kior BV. Borrower shall not permit a Lien on the capital stock of Kior BV, or
pledge the stock certificates of Kior BV, in favor of any other party other than Lender and
Borrower shall take all steps necessary to dissolve the existence of Kior BV within 150 days from
the date of this Agreement.

7. Negative Covenants

Borrower will not do any of the following:

7.1 Location of Collateral. Change its chief executive office or principal place of business or
remove, except in the ordinary course of Borrower’s business, the Collateral or Borrower’s Books
from the premises listed in Section 11 without giving 30 days prior written notice to Agent.

7.2 Extraordinary Transactions. Sell, lease, license or otherwise dispose of its assets, other than
(i) sales of inventory in the ordinary course of Borrower’s business; (ii) licenses of Borrower’s
intellectual property assets entered into in the ordinary course of

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business; and (iii) any other
sale, lease, license or disposition (excluding Collateral hereunder) the net proceeds of which,
does not, taken together with each other sale, lease, license or disposition made in such fiscal
year, exceed $200,000.

7.3 Restructure. Make any material change in Borrower’s financial structure or business operations
(other than through the sale of preferred stock to equity investors which does not result in a
change of control of Borrower); or suspend operation of Borrower’s business.

7.4 Liens. (i) Create, incur, assume or suffer to exist any Lien of any kind with respect to any of
its property, whether now owned or hereafter acquired, except for Permitted Liens, or (ii) enter
into or permit to exist any agreement that restricts the ability of Borrower to grant a Lien to
Agent or Lenders in any of Borrower’s Intellectual Property (as defined in Exhibit A) (other than
restrictions that world be unenforceable or ineffective pursuant to Section 9-408 of the UCC or the
Uniform Commercial Code as adopted in any other applicable jurisdiction).

7.5 Indebtedness. Create, incur, assume or suffer to exist any Indebtedness, other than Permitted
Indebtedness.

7.6 Distributions. Pay any dividends or distributions, or redeem or purchase, any capital stock,
except for (i) repurchases of capital stock from departing employees or directors, under repurchase
agreements approved by the Borrower’s Board of Directors and (ii) dividends or distributions
payable solely in capital stock of Borrower.

7.7 Investments. Acquire or own, or make any Investment in or to any entity, other than Permitted
Investments.

7.8 Transactions with Affiliates. Directly or indirectly enter into any transaction with any affiliate which is on terms less
favorable to Borrower than would be obtained in an arm’s length transaction with a non-affiliated
entity; provided, any such transaction shall not be a breach of this Section 7.7 if approved by a
disinterested majority of the Borrower’s Board of Directors.

7.9 Compliance. (i) Become an “investment company” under the Investment Company Act of 1940 or
extend credit to purchase or carry margin stock; (ii) fail to meet the minimum funding requirements
of ERISA; (iii) permit a Reportable Event or Prohibited Transaction, as defined in ERISA, to occur;
(iv) fail to comply with the Federal Fair Labor Standards Act; or (v) violate any other material
law or material regulation.

7.10 UCC Effectiveness. Change its name, jurisdiction of organization, or take any other action
that could render Lender’s financing statements misleading under the UCC, without giving Lender 30
days advance written notice.

7.11 Deposit and Securities Accounts. Maintain any deposit accounts or accounts holding securities
owned by Borrower except accounts in which Agent on behalf of all Lenders has obtained a perfected
first priority security interest. Notwithstanding the foregoing, Lender shall not have a perfected
security interest in (i) Borrower’s certificate of deposit account no. 0910-00121407355 with Bank
of America which secures Borrower’s commercial credit card facility, provided the amount of such
account shall not exceed 5125,000; (ii) Borrower’s checking account no. 488019490275 with Bank of
America, provided the amount of such account shall not exceed $$2,000,000 and Borrower shall close
such account no later than February 28, 2010 and provide Lender with notice thereof; or (iii)
Borrower’s account no. 3300709750 with Silicon Valley Bank which secures Borrower’s obligations
under a commercial credit card facility, provided the amount of such account shall not exceed
$100,000. For so long as the Obligations are outstanding, Borrower shall not hold directly or
indirectly, purchase or create a purchase order or directive to purchase any auction rate
securities or similar financial instruments regardless of whether such securities are to be held by
Borrower or through one or more brokerage accounts.

7.12 Maintenance of Subsidiaries. Except as set forth in Section 6.10 hereof, Borrower shall not,
and shall not permit or cause any Subsidiary to, (i) sell, dispose of, convey, or allow a Lien to
arise on any of its assets, including Intellectual Property (as defined in Exhibit A) owned by such
Subsidiary (and for this purpose, the definition of intellectual Property” shall be deemed to
refer to such Subsidiary) except for non-exclusive licenses entered into in the ordinary course of
business; (ii) divest or “spin-off” any Subsidiary except where as a result of such transaction
Borrower and/or Borrower’s shareholders or affiliates retain or obtain majority ownership of such
Subsidiary; (iii) merge or consolidate any Subsidiary with or into another entity (unless as a
result of such merger Borrower and/or Borrower’s shareholders or affiliates retain or obtain
majority ownership of the surviving entity); (iv) permit a Change of Control (as defined below) of
any Subsidiary; (v) make a pledge of, any capital stock of any Subsidiary in favor of any person
other than Lender; or (vi) materially change the corporate structure and business operations of the
Borrower and its Subsidiaries taken as a whole. For the purposes of this Section 7.12, a “Change of
Control” shall mean, any transaction or series of related transactions whereby the Borrower and/or
Borrower’s shareholders or affiliates of Borrower holding in excess of 50% of the outstanding
voting capital stock of any Subsidiary immediately prior to such transaction or transactions, shall
own less than 50% of the outstanding voting or capital stock of such Subsidiary immediately
following such transaction or transactions.

8

 

8. Events of Default

Any one or more of the following shall constitute an Event of Default by Borrower hereunder:

8.1 Payment. Borrower fails to pay when due and payable in accordance with the Loan Documents any
portion of the Obligations, or cancels an ACH payment or transfer Lender has initiated in
conformity with the terms hereof provided,, however, that an Event of Default shall not occur on of
a failure to pay due solely to an administrative or operational error if Borrower had the funds to
make the payment when due and makes the payment the business day following Borrower’s knowledge of
such failure to pay.

8.2 Certain Covenant Defaults. Borrower fails to perform any obligation under Section 6.5 or 6.6, or violates any of the
covenants contained in Section 7.

8.3 Other Covenant Defaults. Borrower fails or neglects to perform, keep, or observe any other
term, provision, condition, covenant, or agreement contained in this Agreement, in any of the other
Loan Documents, or in any other present or future agreement between Borrower and Lender and has
failed to cure such failure within 30 days after its occurrence.

8.4 Attachment. Any material portion of Borrower’s assets is attached, seized, subjected to a
government levy, lien, writ or distress warrant, or comes into the possession of any trustee or
receiver and the same is not returned, removed, waived, stayed, discharged or rescinded within 20
days.

8.5 Other Agreements. There is a default in any agreement to which Borrower is a party resulting in
a right by a third party, whether or not exercised, to accelerate the maturity of any Indebtedness,
in an amount greater than $200,000.

8.6 Judgments. One or more judgments for an aggregate of at least $200,000 is rendered against
Borrower and remains unsatisfied and unstayed for more than 30 days.

8.7 Injunction. Borrower is enjoined, restrained, or in any way prevented by court order from
continuing to conduct any material part of its business affairs, or if a judgment or other claim
becomes a Lien upon any material portion of Borrower’s assets.

8.8 Misrepresentation. Any representation, statement, or report made to Lenders by Borrower was
false or misleading when made in any material respect.

8.9 Enforceability. Agent or any Lender’s ability to enforce its rights against Borrower or any
Collateral is impaired in any material respect, or Borrower asserts that any Loan Document is not a
legal, valid and binding obligation of Borrower enforceable in accordance with its terms.

8.10 Involuntary Bankruptcy. An involuntary bankruptcy case remains undismissed or unstayed for 60
days or, if earlier, an order granting the relief sought is entered.

8.11 Voluntary Bankruptcy or Insolvency. Borrower commences a voluntary case under applicable
bankruptcy or insolvency law, consents to the entry of an for relief in an involuntary case under
any such law, or consents or is subject to the appointment of or taking possession by a receiver,
liquidator, assignee, trustee, custodian or other similar official of Borrower or any substantial
part of its property, or makes an assignment for the benefit of creditors, or fails generally or
admits in writing to its inability to pay its debts as they become due, or takes any corporate
action in furtherance of any of the foregoing.

8.12 Merger, Sale or Change of Control. The occurrence of (i) a merger of Borrower with another
entity (whether or not the Borrower is the “surviving entity”) whereby the shareholders of Borrower
immediately prior to such merger own less than 50% of the outstanding voting securities of Borrower
immediately after such merger; (ii) the sale (in one or a series of related transactions) of all or
substantially all of Borrower’s assets;
or (iii) any transaction (or series of related transactions) other than a transaction that is a
bona fide equity financing with the primary purpose of raising capital for Borrower, whereby the
shareholders of Borrower immediately prior to such transaction(s) own less than 50% of the
outstanding voting securities of Borrower immediately after such transaction(s), and such acquirer
or resulting entity (including, Borrower, if Borrower is the resulting or surviving entity) fails
to either: (a) pay off the Obligations in cash at the closing of the acquisition, merger or sale or
(b) provide an unconditional, unlimited guaranty or reaffirmation of the Obligations in form and
substance satisfactory to Lender and is of a credit quality acceptable to Lender.

9. Lender’s Rights and Remedies

9

 

9.1 Rights and Remedies. Upon the occurrence and continuance of any Event of Default, Agent and
Lenders may, at each party’s election, without notice of election and without demand, do any one or
more of the following, all of which are authorized by Borrower: (i) accelerate and declare the Loan
and all Obligations immediately due and payable; (ii) make such payments and do such acts as Agent
or Lenders consider necessary or reasonable to protect Lenders’ security interests in the
Collateral, with such amounts becoming Obligations bearing interest at the Default Rate; (iii)
exercise any and all other rights and remedies available under the UCC or otherwise; (iv) require
Borrower to assemble the Collateral at such places as Agent may designate; (v) enter premises where
any Collateral is located, take, maintain possession of, or render unusable the Collateral or any
part of it; (vi) without notice to Borrower, set off and recoup against any portion of the
Obligations; (vii) ship, reclaim, recover, store, finish, maintain, repair, prepare for sale,
advertise for sale, and sell the Collateral, in connection with which Borrower hereby grants each
Lender a license to use without charge Borrower’s premises, labels, name, trademarks, and other
property necessary to complete, advertise, and sell any Collateral; and (viii) sell the Collateral
at one or more public or private sales.

9.2 Power of Attorney in Respect of the Collateral. Borrower hereby irrevocably appoints Agent
(which appointment is coupled with appointment as its true and lawful attorney in fact with full
power of substitution, for it and in its name to, upon and during the continuance of an Event of
Default: (i) ask, demand, collect, receive, sue for, compound and give acquittance for any and all
Collateral with full power to settle, adjust or compromise any claim, (ii) receive payment of and
endorse the name of Borrower on any items of Collateral, (iii) make all demands, consents and
waivers, or take any other action with respect to, the Collateral, (iv) file any claim or take any
other action, in any Lender’s or Borrower’s name, which Agent may reasonably deem appropriate to
protect its rights in the Collateral, or (v) otherwise act with respect to the Collateral as though
Agent were its outright owner.

9.3 Charges. If Borrower fails to pay any amounts required hereunder to be paid by Borrower to any
third party, Agent may at its option pay any part thereof and any amounts so paid including
Lenders’ Expenses incurred shall become Obligations, immediately due and payable, bearing interest
at the Default Rate, and secured by the Collateral. Any such payments by Agent shall not constitute
an agreement to make similar payments or a waiver of any Event of Default.

9.4 Remedies Cumulative. Agent’s and Lenders’ rights and remedies under the Loan Documents and all
other agreements with Borrower shall be cumulative. Agent and Lenders shall have all other rights
and remedies as provided under the UCC, by law, or in equity. No exercise by Agent or Lenders of
one right or remedy shall be deemed an election, and no waiver by Agent or Lenders of any Event of
Default shall be deemed a continuing waiver. No delay by Agent or any Lender shall constitute a
waiver, election, or acquiescence.

9.5 Application of Collateral Proceeds. Agent and Lenders will apply proceeds of sale, to the
extent actually received in cash, in the manner and order it determines in its sole discretion, and
as prescribed by applicable law.

10. Waivers; Indemnification

10.1 Waivers. Without limiting the generality of the other waivers made by Borrower herein, to the
maximum extent permitted under applicable law, Borrower hereby irrevocably waives all of the
following: (i) any right to assert against Lenders as a defense, counterclaim, set-off
or crossclaim, any defense (legal or equitable), set-off, counterclaim, crossclaim and/or other
claim (a) which Borrower may now or at any time hereafter have against any party liable to Lenders
in any way or manner, or (b) arising directly or indirectly from the present or future lack of
perfection, sufficiency, validity and/or enforceability of any Loan Document, or any security
interest; (ii) presentment, demand and notice of presentment, dishonor, notice of intent to
accelerate, protest, default, nonpayment, maturity, release, compromise, settlement, extension or
renewal of any or all accounts, documents, instruments, chattel paper and guaranties at any time
held by Lenders on which Borrower may in any way be liable and hereby ratifies and confirms
whatever Lender may do in this regard; (iii) the benefit of all marshalling, valuation, appraisal
and exemption laws; (iv) the right, if any, to require Lenders to (a) proceed against any person
liable for any of the Obligations as a condition to or before proceeding hereunder; or (b)
foreclose upon, sell or otherwise realize upon or collect or apply any other property, real or
personal, securing any of the Obligations, as a condition to, or before proceeding hereunder; (v)
any demand for possession before the commencement of any suit or action to recover possession of
Collateral; and (vi) any requirement that Lenders retain possession and not dispose of Collateral
until after trial or final judgment.

10.2 Lenders’ Liability for Collateral. Lenders shall not in any way or manner be liable or
responsible for: (i) the safekeeping of any Collateral; (ii) any loss or damage thereto occurring
or arising in any manner or fashion from any cause; (iii) any diminution in the value thereof, or
(iv) any act or default of any carrier, warehouseman, bailee, forwarding agency, or other person or
entity whomsoever. All risk of loss, damage or destruction of the Collateral shall be borne by
Borrower. Lenders will have no responsibility for taking any steps to preserve rights against any
parties respecting any Collateral. Lenders’ powers hereunder are conferred solely to protect its
interest in the Collateral and do not impose any duty to exercise any such powers. None of Lenders
or any of its officers, directors, employees, agents or counsel will be liable for any action
lawfully taken or omitted to be taken

10

 

hereunder or in connection herewith (excepting gross
negligence or willful misconduct), nor under any circumstances have any liability to Borrower for
lost profits or other special, indirect, punitive, or consequential damages. Lenders retain any
documents delivered by Borrower only for their purposes and for such period as each Lender, at its
sole discretion, may determine necessary, after which time such Lender may destroy such records
without notice to or consent from Borrower.

10.3 Indemnification. Borrower shall, on an after tax basis, defend, indemnify, and hold each
Lender and each of its officers, directors, employees, counsel, partners, agents and
attorneys-in-fact (each, an “Indemnified Person”) harmless from and against any and all
liabilities, obligations, losses, damages, penalties, actions, judgments, suits, costs, charges,
expenses or disbursements (including Lenders’ Expenses and reasonable attorney’s fees) of any kind
or nature whatsoever with respect to the execution, delivery, enforcement, performance and
administration of this Agreement and any other Loan Documents, or the transactions contemplated
hereby and thereby, with respect to noncompliance with laws or regulations respecting Regulated
Substances, government secrecy or technology export, or any Lien not created by a Lender or right
of another against any Collateral, even if the Collateral is foreclosed upon or sold pursuant
hereto, and with respect to any investigation, litigation or proceeding before any agency, court or
other governmental authority relating to this Agreement or the Advances or the use of the proceeds
thereof, whether or not any Indemnified Person is a party thereto (all the foregoing, collectively,
the “Indemnified Liabilities”); provided, that Borrower shall have no obligation hereunder to any
Indemnified Person with respect to Indemnified Liabilities arising from the gross negligence or
willful misconduct of such Indemnified Person. The obligations in this Section shall survive the
Term. At the election of any Indemnified Person, Borrower shall defend such Indemnified Person
using legal counsel reasonably satisfactory to such Indemnified Person, at the sole cost and
expense of Borrower. All amounts owing under this Section shall be paid within 30 days after
written demand.

11. Notices

All notices shall be in writing and personally delivered or sent by certified mail, postage
prepaid, return receipt requested, or by confirmed facsimile, at the respective addresses set forth
below:

	 	 	 

	If to Borrower:

	 	If to Agent:
	 
	Kior, Inc.

	 	Lighthouse Capital Partners VI, L.P.
	Attention: Chief Financial Officer

	 	Attention: Contract Administrator
	13001 Bay Park Road

	 	3555 Alameda de las Pulgas, Suite 200
	Pasadena, Texas 77507

	 	Menlo Park, California 94025
	FAX: (281) 694-8799

	 	FAX: (650) 233-0114

	 	 	If to any Lender, to the address set forth on Schedule A hereto.

12. General Provisions

12.1 Successors and Assigns. This Agreement shall bind and inure to the benefit of the parties’
respective successors and permitted assigns. Borrower may not assign any rights hereunder without
Agent’s prior written consent, which consent may be granted or withheld in Agent’s sole discretion.
Each Lender shall have the right without the consent of or notice to Borrower to sell, transfer,
negotiate, or grant participations in all or any part of any Loan Agreement, except for any such
sale, transfer, negotiation or grant of a participation to a competitor of Borrower or any of its
Subsidiaries.

12.2 Time of Essence. Time is of the essence for the performance of all Obligations.

12.3 Severability of Provisions. Each provision hereof shall be severable from every other
provision in determining its legal enforceability.

12.4 Entire Agreement. This Agreement and each of the other Loan Documents dated as of the date
hereof, taken together, constitute and contain the entire agreement between Borrower and Lenders
with respect to their subject matter and supersede any and all prior agreements, negotiations,
correspondence, understandings and communications between the parties, whether written or oral.
This Agreement is the result of negotiations between and has been reviewed by the Borrower and
Lenders as of the date hereof and their respective counsel; accordingly, this Agreement shall be
deemed to be the product of the parties hereto, and no ambiguity shall be construed in favor of or
against Borrower or Lender. The provision of any Loan Document may be modified, amended or waived
only by a written instrument signed by the parties thereto. Any waiver or consent with respect to
any provision of the Loan Documents shall be effective only in the specific instance and for the
specific purpose for which it was given. No notice to or demand on in any one case shall entitle
Borrower to any other or further notice or demand in similar or other circumstances.

11

 

12.5 Reliance by Lenders. All covenants, agreements, representations and warranties made herein by
Borrower shall, notwithstanding any investigation by any Lender, be deemed to be material to and to
have been relied upon by each Lender.

12.6 No Set-Offs by Borrower. All sums payable by Borrower pursuant to this Agreement or any of the
other Loan Documents shall be payable without notice or demand and shall be payable in United
States Dollars without set-off or reduction of any manner whatsoever.

12.7 Counterparts. This Agreement may be executed in any number of counterparts, each of which
shall be deemed to be an original, and all of which, when taken together, shall constitute one and
the same original instrument.

12.8 Survival. All covenants, representations and warranties made in this Agreement shall continue
in full force and effect so long as any Obligations remain outstanding.

12.9 No Original issue Discount. Borrower and Lenders acknowledge and agree that the Warrant is
part of an investment unit within the meaning of Section 1273(c)(2) of the Internal Revenue Code,
which includes the Loan. Borrower and Lenders further agree as between them, that the fair market
value of each Warrant is $100 and that, pursuant to Treas. Reg. § 1.1273-2(h), $100 of the issue
price of the investment unit will be allocable to the Warrant and the balance shall be allocable to
the Loans. Borrower and Lenders agree to prepare their
respective federal income tax returns in a manner consistent with the foregoing and, pursuant to
Treas. Reg, § 1. 1273, the original issue discount on the Loan shall be considered to be zero.

12.10 Relationship of Parties. The relationship between Borrower and each Lender is, and at all
times shall remain, solely that of a borrower and lender. No Lender is a partner or joint venturer
of Borrower; nor shall any Lender under any circumstances be deemed to be in a relationship of
confidence or trust or have a fiduciary relationship with Borrower or any of its affiliates, or to
owe any fiduciary duty to Borrower or any of its affiliates. No Lender undertakes or assumes any
responsibility or duty to Borrower or any of its affiliates to select, review, inspect, supervise,
pass judgment upon or otherwise inform any of them of any matter in connection with its or their
property, the Loans, any Collateral or the operations of Borrower or any of its affiliates.
Borrower and each of its affiliates shall rely entirely on their own judgment with respect to such
matters, and any review, inspection, supervision, exercise of judgment or supply of information
undertaken or assumed by any Lender in connection with such matters is solely for the protection of
such Lender and neither Borrower nor any affiliate is entitled to rely thereon.

12.11 Choice of Law and Venue; Jury Trial Waiver. THIS AGREEMENT SHALL BE GOVERNED BY AND CONSTRUED
IN ACCORDANCE WITH, THE INTERNAL LAWS OF THE STATE OF CALIFORNIA, WITHOUT REGARD TO PRINCIPLES OF
CONFLICTS OF LAW. EACH OF BORROWER AND LENDER HEREBY SUBMITS TO THE EXCLUSIVE JURISDICTION AND
VENUE OF THE STATE AND FEDERAL COURTS LOCATED IN THE CITY AND COUNTY OF SAN FRANCISCO, STATE OF
CALIFORNIA. BORROWER AND EACH LENDER HEREBY WAIVE THEIR RESPECTIVE RIGHTS TO A JURY TRIAL OF ANY
CLAIM OR CAUSE OF ACTION BASED UPON OR ARISING OUT OF ANY OF THE LOAN DOCUMENTS OR ANY OF THE
TRANSACTIONS CONTEMPLATED THEREIN, INCLUDING CONTRACT CLAIMS, TORT CLAIMS, BREACH OF DUTY CLAIMS,
AND ALL OTHER COMMON LAW OR STATUTORY CLAIMS. EACH PARTY FURTHER WAIVES ANY RIGHT TO CONSOLIDATE
ANY ACTION IN WHICH A JURY TRIAL HAS BEEN WAIVED WITH ANY OTHER ACTION IN WHICH A JURY TRIAL CANNOT
BE OR HAS NOT BEEN WAIVED.

In Witness Whereof, the parties hereto have executed this Agreement as of the date first above written.

	 	 	 	 	 	 	 	 	 
	Borrower:	 	Agent:	 	 
	 
	Kior, Inc.	 	Lighthouse Capital Partners VI, L.P.	 	 
	 

	 	 	 	By:
	 	Lighthouse Management Partners VI, L.L.C., 

its general partner	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	/s/ Fred Cannon
 

	 	By:
	 	/s/ Cristy Barnes
 

	 	 
	Name: Fred Cannon	 	Name: Cristy Barnes	 	 
	Title: Pres.	 	Title: Managing Director	 	 

12

 

	 	 	 	 	 	 	 	 	 
	Lenders:	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	LEADER LENDING, LLC — SERIES A	 	LEADER LENDING, LLC — SERIES B	 	 
	By:	 	Leader Ventures, LLC, its Manager	 	By: Leader Ventures, LLC, its Manager	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	/s/ Robert W. Molke
 

	 	By:
	 	/s/Robert W. Molke
 

	 	 
	Name: Robert W. Molke	 	Name: Robert W. Molke	 	 
	Title: Managing Director	 	Title: Managing Director	 	 
	 
	 	 	 	 	 	 	 	 
	Lighthouse Capital Partners VI, L.P.	 	 	 	 	 	 
	By:

	 	Lighthouse Management Partners VI, L.L.C.,

its general partner	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By:
	 	 	 	 	 	 	 	 
	Name:

	 	 	 	 	 	 	 	 
	Title:
	 	 	 	 	 	 	 	 

	 	 	 

	Schedule A

	 	Lenders (Name, Address and Percentage Interests)
	 
	Exhibit A

	 	Collateral Description
	Exhibit B

	 	Form of Note
	Exhibit C

	 	Form of Preferred Stock Warrant
	Exhibit C- 1

	 	Form of Tranche 2 Warrant
	Exhibit D

	 	Form of Notice of Borrowing
	Exhibit E

	 	Form of Incumbency Certificate
	Exhibit F

	 	Form of Officers Certificate
	Exhibit G

	 	ACH Authorization
	Exhibit H

	 	Form of Negative Pledge Agreement
	Exhibit I

	 	Control Agreement
	Schedule 1

	 	Disclosure Schedule

13exv4w12

Exhibit 4.12

AMENDMENT NO. 01

Dated June 30, 2010

     THIS AMENDMENT NO l (“Amendment No. 1”) to that certain Loan and Security Agreement No. 1452
dated as of January 27, 2010 (“Agreement”), by and between Lighthouse Capital Partners VI,
L.P., as “Agent” for the lenders identified on
Schedule A to the Agreement (such
lenders, together with their respective successors and assigns are referred to herein each
individually as a “Lender” and collectively as “Lenders”), the Lenders and Kior, Inc.
(“Borrower”).

(All capitalized terms not otherwise defined herein shall have the meanings given to such terms in
the Agreement.)

Without limiting or amending any other provisions of the Agreement, Lender and Borrower agree to
the following:

Section 6.10 of the Agreement, the following definition shall be deleted in its entirety and
replaced with the following:

6.10 Dissolution of Kior BV. Borrower shall not permit a Lien on the capital stock of Kior BV, or
pledge the stock certificates of Kior BV, in favor of any other party other than Lender and
Borrower shall take all steps necessary to dissolve the existence of Kior BV no later than October
31, 2010.

Execution and delivery of this Amendment constitutes a reaffirmation as of the date thereof of all
of the representations and warranties contained in the Agreement and the Loan Documents, as such
representations and warranties may be amended hereby.

Except as amended hereby, the Agreement remains unmodified and unchanged.

	 	 	 	 	 	 	 	 	 	 	 

	BORROWER:	 	 	 	AGENT:	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Kior, Inc.	 	 	 	Lighthouse Capital Partners V, L.P.	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By: 

Name:
Title:

	 	/s/ George E. Staggs
 

George E. Staggs
Treasurer & Controller
	 	 	 	By:
	 	Lighthouse management
Partners V, L.L.C., 
its general partner
	 	 
	 
	 	 	 	 	 	By:

Name:
Title:
	 	/s/ Cristy Barnes
 

Cristy Barnes
Managing Director
	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	Lenders:	 	 	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	LEADER LENDING, LLC — SERIES A	 	 	 	LEADER LENDING, LLC — SERIES B	 	 
	 
	 	 	 	 	 	 	 	 	 	 
	By: 

Name:

	 	/s/ Robert W. Molke
 

Robert W. Molke
	 	 	 	By:

Name:
	 	/s/ Robert W. Molke
 

Robert W. Molke
	 	 
	Title:

	 	Managing Director
	 	 	 	Title:
	 	Managing Director	 	 

 

 

	 	 	 	 	 	 	 	 	 

	Lighthouse Capital Partners VI, L.P.	 	 	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	Lighthouse Management Partners VI L.L.C., 

its general partner
	 	
	 	 	 	 
	 
	 	 	 	 	 	 	 	 
	By:

	 	/s/ Cristy Barnes	 	 	 	 	 	 
	 

	 	 	 	 	 	 	 	 
	Name:

	 	Cristy Barnes	 	 	 	 	 	 
	Title:

	 	Managing Director

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