CODEXIS, INC. — Major Shareholding Notification 2019

Feb 14, 2019

SC 13G/A 1 tv513648_sc13ga.htm SCHEDULE 13G/A

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UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13G

Under the Securities Exchange Act of 1934

(Amendment No. 6)*

Codexis, Inc.

(Name of Issuer)

Common Stock, par value $0.0001 per share

(Title of Class of Securities)

192005106

(CUSIP Number)

December 31, 2018

(Date of Event Which Requires Filing of this Statement)

Check the appropriate box to designate the rule pursuant to which this Schedule is filed:

x	Rule 13d-1(b)
¨	Rule 13d-1(c)
¨	Rule 13d-1(d)

*The remainder of this cover page shall be filled out for a reporting person's initial filing on this form with respect to the subject class of securities, and for any subsequent amendment containing information which would alter the disclosures provided in a prior cover page.

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

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Page 1 of 7 Pages

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CUSIP NO. 192005106 Page 2 of 7 Pages

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CUSIP No. 192005106
(1)
Names of reporting persons	Nantahala
Capital Management, LLC
(2)
Check the appropriate box if a member of a group	(a)
(see
instructions)	(b)
(3)
SEC use only
(4)
Citizenship or place of organization	MA
Number
of shares beneficially owned by each reporting person with:
(5)
Sole voting power	0
(6)
Shared voting power	6,549,800
(7)
Sole dispositive power	0
(8)
Shared dispositive power	6,549,800
(9)
Aggregate amount beneficially owned by each reporting person	6,549,800
(10)
Check if the aggregate amount in Row (9) excludes certain shares (see instructions)
(11)
Percent of class represented by amount in Row (9)	12.1%
(12)
Type of reporting person (see instructions)	IA

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CUSIP NO. 192005106 Page 3 of 7 Pages

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CUSIP No. 192005106
(1)
Names of reporting persons	Wilmot
B. Harkey
(2)
Check the appropriate box if a member of a group	(a)
(see
instructions)	(b)
(3)
SEC use only
(4)
Citizenship or place of organization	USA
Number
of shares beneficially owned by each reporting person with:
(5)
Sole voting power	0
(6)
Shared voting power	6,549,800
(7)
Sole dispositive power	0
(8)
Shared dispositive power	6,549,800
(9)
Aggregate amount beneficially owned by each reporting person	6,549,800
(10)
Check if the aggregate amount in Row (9) excludes certain shares (see instructions)
(11)
Percent of class represented by amount in Row (9)	12.1%
(12)
Type of reporting person (see instructions)	HC

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CUSIP NO. 192005106 Page 4 of 7 Pages

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CUSIP No. 192005106
(1)
Names of reporting persons	Dan
Mack
(2)
Check the appropriate box if a member of a group	(a)
(see
instructions)	(b)
(3)
SEC use only
(4)
Citizenship or place of organization	USA
Number
of shares beneficially owned by each reporting person with:
(5)
Sole voting power	0
(6)
Shared voting power	6,549,800
(7)
Sole dispositive power	0
(8)
Shared dispositive power	6,549,800
(9)
Aggregate amount beneficially owned by each reporting person	6,549,800
(10)
Check if the aggregate amount in Row (9) excludes certain shares (see instructions)
(11)
Percent of class represented by amount in Row (9)	12.1%
(12)
Type of reporting person (see instructions)	HC

Item 1(a).	Name of Issuer:
	Codexis, Inc. (the “Iss uer”).
Item 1(b).	Address of the Issuer's Principal Executive
Offices:
	200 Penobscot Drive, Redwood City, California
94063
Item 2(a).	Name of Person Filing
	Nantahala
Capital Management, LLC (“Nantahala”) Wilmot B. Harkey Daniel Mack (together the “Reporting Persons”)
Item 2(b).	Address of Principal Business Office
or, if None, Residence:
	19
Old Kings Highway S, Suite 200 Darien, CT 06820

Item 2(c).	Citizenship:
	Nantahala
is a Massachusetts limited liability company. Each of Messrs. Harkey and Mack is a citizen of the
United States of America.
Item 2(d).	Title
of Class of Securities:
	Common Stock, par value $0.0001 per share (the “Shares”).

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CUSIP NO. 192005106 Page 5 of 7 Pages

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| Item 2(e). | CUSIP
Number: |
| --- | --- |
| | 192005106 |
| Item 3. | If
this statement is filed pursuant to Rule 13d-1(b), or 13d-2(b) or (c), check whether
the person filing is a: |
| | (a) ¨ Broker or dealer registered under
section 15 of the Act (15 U.S.C. 78o). (b) ¨ Bank as defined in section 3(a)(6) of the Act (15 U.S.C. 78c). (c) ¨ Insurance company as defined in section 3(a)(19) of the Act (15 U.S.C. 78c). (d) ¨ Investment company registered under section 8 of the Investment Company Act of 1940 (15 U.S.C 80a-8). (e) x An investment adviser in accordance with §240.13d-1(b)(1)(ii)(E). (f) ¨ An employee benefit plan or endowment fund in accordance with §240.13d-1(b)(1)(ii)(F). (g) x A parent holding company or control person in accordance with § 240.13d-1(b)(1)(ii)(G). (h) ¨ A savings associations as defined in Section 3(b) of the Federal Deposit Insurance Act (12 U.S.C. 1813). (i) ¨ A church plan that is excluded from the definition of an investment company under section 3(c)(14) of the Investment Company Act of 1940 (15 U.S.C. 80a-3). (j) ¨ Group, in accordance with §240.13d-1(b)(1)(ii)(J). |
| Item 4. | Ownership: |
| Item 4(a). | Amount
Beneficially Owned: As of December 31, 2018, Nantahala may
be deemed to be the beneficial owner of 6,549,800 Shares held by funds and separately managed accounts under its control, and
as the managing members of Nantahala, each of Messrs. Harkey and Mack may be deemed to be a beneficial owner of those Shares. |
| Item 4(b). | Percent
of Class: As of December 31, 2018, each of the Reporting
Persons may be deemed to be the beneficial owner of 12.1% of the total number of Shares outstanding (based upon information provided
by the Issuer on Form 10-Q filed November 09, 2018, there were 54,016,098 Shares outstanding as of October 31, 2018). |

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CUSIP NO. 192005106 Page 6 of 7 Pages

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Item 4(c).
Nantahala
Capital Management, LLC
(i)	Sole
power to vote or direct the vote	0
(ii)	Shared
power to vote or to direct the vote	6,549,800
(iii)	Sole
power to dispose or to direct the disposition of	0
(iv)	Shared
power to dispose or to direct the disposition of	6,549,800
Each of Messrs. Harkey and Mack:
(i)	Sole
power to vote or direct the vote	0
(ii)	Shared power to vote
or to direct the vote	6,549,800
(iii)	Sole power to dispose
or to direct the disposition of	0
(iv)	Shared power to dispose
or to direct the disposition of	6,549,800

| Item 5. | Ownership of Five Percent
or Less of a Class: |
| --- | --- |
| | This
Item 5 is not applicable. |
| Item 6. | Ownership of More than Five Percent
on Behalf of Another Person: |
| | Nantahala Capital Partners SI, LP, a fund
advised by Nantahala, has the right to receive or the power to direct the receipt of dividends from, or the proceeds from
the sale of, approximately 6.6% of the outstanding shares of common stock beneficially owned by Nantahala reported herein. |
| Item 7. | Identification and Classification of
the Subsidiary Which Acquired the Security Being Reported on by the Parent Holding Company: |
| | Each of Messrs. Harkey and Mack is filing
this Schedule 13G as a control person in respect of shares beneficially owned by Nantahala, an investment adviser as described
in §240.13d-1(b)(1)(ii)(E). See Item 4(a). |
| Item 8. | Identification and Classification of
Members of the Group: |
| | This Item 8 is not applicable. |
| Item 9. | Notice of Dissolution of Group: |
| | This Item 9 is not applicable. |

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CUSIP NO. 192005106 Page 7 of 7 Pages

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ITEM 10. Certification:

By signing below each Reporting Person certifies that, to the best of such person's knowledge and belief, the securities referred to above were acquired and are held in the ordinary course of business and were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having such purpose or effect.

SIGNATURES

After reasonable inquiry and to the best of my knowledge and belief, the undersigned certifies that the information set forth in this statement is true, complete, and correct.

Date: February 14, 2019
By:	/s/ Paul E. Rehm
	Paul E. Rehm
	Chief Compliance Officer
/s/ Wilmot
B. Harkey
Wilmot B. Harkey
/s/ Daniel Mack
Daniel Mack

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