Immune Design SC 13D/A .

Immune Design Inactive SC 13D/AImmune Design Corp.

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 4)

Immune Design Corp.

(Name of Issuer)

Common Stock, $0.001 par value

(Title of Class of Securities)

45252L 103

(CUSIP Number)

Peter Svennilson

The Column Group, LP

1700 Owens Street, Suite 500

San Francisco, CA 94158

(415)865-2050

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

November 30, 2018

(Date of Event which Requires Filing of this Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of§§ 240.13d-1(e),240.13d-1(f) or240.13d-1(g), check the following box. ☐

Note: Schedules filed in paper format shall include a signed original and five copies of the schedule, including all exhibits. See§240.13d-7 for other parties to whom copies are to be sent.

*	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 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, as amended (“Securities Exchange Act”) or otherwise subject to the liabilities of that section of the Securities Exchange Act but shall be subject to all other provisions of the Securities Exchange Act (however, see the Notes).

CUSIP No. 45252L 103


1.		Name of Reporting Person The Column Group, LP
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(1)

The Column Group, LP (“TCG LP”) has sole voting and dispositive control over 3,161,942 shares of common stock, par value $0.001 per share (“Common Stock”), of Immune Design Corp. (the “Issuer”), except that The Column Group GP, LP (“TCG GP”), the general partner of TCG LP, and Peter Svennilson (“Svennilson”) and David V. Goeddel (“Goeddel”), the managing partners of TCG GP, may be deemed to share dispositive and voting power over such stock.

(2)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person The Column Group GP, LP
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(3)	TCG GP is the general partner of TCG LP and shares voting and dispositive power over the shares of Common Stock held by TCG LP.

(4)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person The Column Group II, LP
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(5)

The Column Group II, LP (“TCG II LP”) has sole voting and dispositive control over 800,000 shares of Common Stock, except that The Column Group II GP, LP (“TCG II GP”), the general partner of TCG II LP, and Svennilson and Goeddel, the managing partners of TCG II GP, may be deemed to share dispositive and voting power over such stock.

(6)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person The Column Group II GP, LP
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(7)	TCG II GP is the general partner of TCG II LP and shares voting and dispositive power over the shares of Common Stock held by TCG II LP.

(8)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person Ponoi Capital, LP
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): WC
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(9)

Ponoi Capital, LP (“Ponoi LP”) has sole voting and dispositive control over 2,681,000 shares of Common Stock, except that Ponoi Management, LLC (“Ponoi LLC”), the general partner of Ponoi LP, and Svennilson, Goeddel and Tim Kutzkey (“Kutzkey”), the managing partners of Ponoi LLC, may be deemed to share dispositive and voting power over such stock.

(10)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person Ponoi Management, LLC
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Delaware

(11)	Ponoi LLC is the general partner of Ponoi LP and shares voting and dispositive power over the shares of Common Stock held by Ponoi LP.

(12)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person Peter Svennilson
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: Sweden

(13)	Svennilson is a managing partner of TCG GP, TCG II GP and Ponoi LLC and may be deemed to share voting and dispositive control over the shares of Common Stock held by TCG LP, TCG II LP and Ponoi LP.

(14)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person David V. Goeddel
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: U.S.A.

(15)	Goeddel is a managing partner of TCG GP, TCG II GP and Ponoi LLC and may be deemed to share voting and dispositive control over the shares of Common Stock held by TCG LP, TCG II LP and Ponoi LP.

(16)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

CUSIP No. 45252L 103


1.		Name of Reporting Person Tim Kutzkey
2.		Check the Appropriate Box if a Member of a Group (See Instructions) (a) ☐ (b) ☒
3.		SEC Use Only:
4.		Source of Funds (See Instructions): AF
5.		Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e): ☐
6.		Citizenship or Place of Organization: U.S.A.

(17)	Kutzkey is a managing partner of Ponoi LLC and may be deemed to share voting and dispositive control over the shares of Common Stock held by Ponoi LP.

(18)	The percentage set forth in row (13) is based on 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

SCHEDULE 13D

Item 1. Security and Issuer

This Amendment No. 4 supplements and amends the Schedule 13D that was originally filed on August 4, 2014 (the “Initial Statement”), as amended by Amendment No. 1 to Schedule 13D that was filed on April 23, 2015, Amendment No. 2 to Schedule 13D that was filed on September 22, 2016 and Amendment No. 3 to Schedule 13D that was filed on October 30, 2017 (the “Amended Statement”), to reflect changes resulting from (a) an increase in the number of outstanding shares of Common Stock of the Issuer and (b) the expiration of options to purchase shares of the Issuer’s Common Stock held by Mr. Svennilson. Only those items that are reported are hereby amended; all other items reported in the Amended Statement remain unchanged. Information given in response to each item shall be deemed incorporated by reference in all other items as applicable.

Item 2. Identity and Background

Items 2(a) and (c) of the Amended Statement and Item 2(f) of the Initial Statement are hereby amended and restated in their entirety as follows:

(a) This Schedule 13D is being filed by (i) The Column Group, LP, a Delaware limited partnership (“TCG LP”), (ii) The Column Group GP, LP, a Delaware limited partnership (“TCG GP”), (iii) The Column Group II, LP, a Delaware limited partnership (“TCG II LP”), (iv) The Column Group II GP, LP, a Delaware limited partnership (“TCG II GP”), (v) Ponoi Capital, LP, a Delaware limited partnership (“Ponoi LP”), (vi) Ponoi Management, LLC, a Delaware limited liability company (“Ponoi LLC”) and (vii) Peter Svennilson, David V. Goeddel and Tim Kutzkey (collectively referred to as the “Managing Partners”). Mr. Svennilson and Mr. Goeddel are the Managing Partners of TCG GP and TCG II GP, and Mr. Svennilson, Mr. Goeddel and Mr. Kutzkey are the Managing Partners of Ponoi LLC. The Managing Partners, TCG LP, TCG GP, TCG II LP, TCG II GP, Ponoi LP and Ponoi LLC are sometimes hereinafter collectively referred to as the “Reporting Persons.”

(c) The principal business of each of TCG LP, TCG II LP and Ponoi LP is making venture capital investments. TCG GP’s principal business is acting as general partner of TCG LP. TCG II GP’s principal business is acting as general partner of TCG II LP. Ponoi LLC’s principal business is acting as general partner of Ponoi LP. Each of Mr. Svennilson’s and Mr. Goeddel’s principal business is acting as a managing partner of TCG GP, TCG II GP and Ponoi LLC and of The Column Group III GP, LP and Ponoi II Management LLC (“Ponoi II LLC”), affiliates of TCG GP, TCG II GP and Ponoi LLC. Mr. Kutzkey’s principal business is acting as a managing partner of Ponoi LLC and Ponoi II LLC.

(f) Mr. Svennilson is a citizen of Sweden, and Mr. Goeddel and Mr. Kutzkey are citizens of the United States.

Item 3. Source and Amount of Funds or Other Consideration

Item 3 of the Amended Statement is hereby amended by deleting the first paragraph and adding the following in lieu thereof:

As consideration for his service as a director of the Issuer, Mr. Svennilson received options to purchase 52,720 shares of Common Stock (the “Options”). Mr. Svennilson resigned as a director of the Issuer effective August 31, 2018 and the Options expired unexercised on November 30, 2018.

Item 5. Interest in Securities of the Issuer

Items 5(a), (b) and (c) of the Amended Statement are hereby amended and restated in their entirety as follows:

(a) As of the date hereof, TCG LP directly holds 3,161,942 shares of Common Stock, representing 6.6% of the Issuer’s outstanding Common Stock. As the general partner of TCG LP, TCG GP beneficially owns an aggregate of 3,161,942 shares of Common Stock, representing 6.6% of the Issuer’s outstanding Common Stock. TCG II LP directly holds 800,000 shares of Common Stock, representing 1.7% of the Issuer’s outstanding Common Stock. As the general partner of TCG II LP, TCG II GP beneficially owns an aggregate of 800,000 shares of Common Stock, representing 1.7% of the Issuer’s outstanding Common Stock. Ponoi LP directly holds 2,681,000 shares of Common Stock, representing 5.6% of the Issuer’s outstanding Common Stock. As the general partner of Ponoi LP, Ponoi LLC beneficially owns an aggregate of 2,681,000 shares of Common Stock, representing 5.6% of the Issuer’s outstanding

Common Stock. Mr. Svennilson, as a Managing Partner of TCG GP, TCG II GP and Ponoi LLC, beneficially owns 6,642,942 shares of Common Stock, representing 13.8% of the Issuer’s outstanding Common Stock. Mr. Goeddel, as a Managing Partner of TCG GP, TCG II GP and Ponoi LLC, beneficially owns 6,642,942 shares of Common Stock, representing 13.8% of the Issuer’s outstanding Common Stock. Mr. Kutzkey, as a Managing Partner of Ponoi LLC, beneficially owns 2,681,000 shares of Common Stock, representing 5.6% of the Issuer’s outstanding Common Stock.

The percentages set forth in this Item 5 are based on the 48,164,828 outstanding shares of Common Stock as of November 5, 2018, as disclosed in the Issuer’s Quarterly Report on Form10-Q filed with the SEC on November 6, 2018.

(b) TCG LP has sole voting and dispositive control over 3,161,942 shares of Common Stock, TCG II LP has sole voting and dispositive control over 800,000 shares of Common Stock and Ponoi LP has sole voting and dispositive control over 2,681,000 shares of Common Stock. None of the other Reporting Persons own any securities of the Issuer directly. TCG GP, as general partner of TCG LP, shares the power to direct the voting and disposition of the 3,161,942 shares owned by TCG LP and may be deemed to beneficially own the shares owned by TCG LP. TCG II GP, as general partner of TCG II LP, shares the power to direct the voting and disposition of the 800,000 shares owned by TCG II LP and may be deemed to beneficially own the shares owned by TCG II LP. Ponoi LLC, as general partner of Ponoi LP, shares the power to direct the voting and disposition of the 2,681,000 shares owned by Ponoi LP and may be deemed to beneficially own the shares owned by Ponoi LP. By virtue of their positions as managing partners of TCG GP and TCG II GP, each of Mr. Svennilson and Mr. Goeddel may be deemed to share the power to direct the voting and disposition of the 3,161,942 shares owned by TCG LP and the 800,000 shares owned by TCG II LP and may be deemed to beneficially own the shares owned by such entities. By virtue of their positions as managing partners of Ponoi LLC, each Managing Partner may be deemed to share the power to direct the voting and disposition of the 2,681,000 shares owned by Ponoi LP and may be deemed to beneficially own the shares owned by Ponoi LP.

(c) On January 4, 2018, Mr. Svennilson, as a director of the Issuer, received options to purchase 12,500 shares of the Issuer’s Common Stock at an exercise price of $4.05 per share and exercisable on January 4, 2019, however, Mr. Svennilson retired as a director of the Issuer effective August 31, 2018 and all of the 52,720 options (the “Options”) to purchase shares of Issuer Common Stock held by him expired unexercised on November 30, 2018. In addition to the 12,500 options received on January 4, 2018, the Options include those received in the following transactions: on January 4, 2017, Mr. Svennilson, as a director of the Issuer, received options to purchase 10,000 shares of the Issuer’s Common Stock at an exercise price of $5.60 per share and exercisable on January 4, 2018; on January 4, 2016, Mr. Svennilson, as a director of the Issuer, received options to purchase 9,300 shares of the Issuer’s Common Stock at an exercise price of $19.39 per share and exercisable on January 4, 2017; on January 7, 2015, Mr. Svennilson, as a director of the Issuer, received options to purchase 9,300 shares of the Issuer’s Common Stock at an exercise price of $31.00 per share and exercisable on January 1, 2016; on June 27, 2014, Mr. Svennilson, as a director of the Issuer, received options to purchase 7,339 shares of the Issuer’s Common Stock at an exercise price of $8.92 per share and exercisable on June 27, 2015; and on December 19, 2013, Mr. Svennilson, as a director of the Issuer, received options to purchase 4,281 shares of the Issuer’s Common Stock at an exercise price of $1.23 per share and exercisable on December 19, 2014.

Item 6. Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer.

Item 6 of the Initial Statement is hereby amended by deleting the second to last paragraph and adding the following in lieu thereof:

Mr. Svennilson, in his capacity as a director of the Issuer, and along with the other directors of the Issuer, entered into an indemnification agreement with the Issuer providing for indemnification to the fullest extent permitted by applicable law and the Issuer’s amended and restated bylaws. These indemnification agreements provide, among other things, that the Issuer will indemnify the directors and certain former directors for certain expenses, including damages, judgments, fines, penalties, settlements and costs and attorneys’ fees and disbursements, incurred by a director in any claim, action, or proceeding arising in his or her capacity as a director of the Issuer or in connection with service at the Issuer’s request for another corporation or entity. The indemnification agreements also provide for procedures that will apply in the event that a director makes a claim for indemnification. The indemnification

agreement terminates upon the later of (a) ten years after the date the indemnitee has ceased to serve as a director of the Issuer or (b) one year after the final termination of any pending proceeding in which the indemnitee is granted indemnification or advancement rights under the indemnification agreement and of any proceeding commenced by the indemnitee under the agreement relating thereto. This summary description does not purport to be complete, and is qualified in its entirety by the Form of Indemnification Agreement, a copy of which is filed as exhibit 10.14 to theS-1 and is incorporated by reference.

Item 7. Material to be filed as Exhibits

Item 7 of the Amended Statement is hereby amended to replace Exhibit A as follows:

A. Joint Filing Statement.

SIGNATURE

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


Dated: February 19, 2019

THE COLUMN GROUP, LP		THE COLUMN GROUP GP, LP

By:	The Column Group GP, LP

By:	/s/ Peter Svennilson	By:	/s/ Peter Svennilson
Name:	Peter Svennilson	Name:	Peter Svennilson
Title:	Managing Partner	Title:	Managing Partner

THE COLUMN GROUP II, LP		THE COLUMN GROUP II GP, LP

By:	The Column Group II GP, LP

By:	/s/ Peter Svennilson	By:	/s/ Peter Svennilson
Name:	Peter Svennilson	Name:	Peter Svennilson
Title:	Managing Partner	Title:	Managing Partner

PONOI CAPITAL, LP		PONOI MANAGEMENT, LLC

By:	Ponoi Management, LLC

By:	/s/ Peter Svennilson	By:	/s/ Peter Svennilson
Name:	Peter Svennilson	Name:	Peter Svennilson
Title:	Managing Partner	Title:	Managing Partner

By:	/s/ Peter Svennilson
	Peter Svennilson

By:	/s/ David V. Goeddel
	David V. Goeddel

By:	/s/ Tim Kutzkey
	Tim Kutzkey

Number of
Shares
Beneficially
by
Owned by
Each
Reporting
Person
With

Sole Voting Power:

3,161,942(1)

Shared Voting Power:

0

Sole Dispositive Power:

3,161,942(1)

Shared Dispositive Power:

0