Column Group Ii SC 13D/A RAPT Therapeutics / COLUMN GROUP II ownership change

Column Group Ii SC 13D/ARAPT Therapeutics / COLUMN GROUP II ownership change

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 6)*

RAPT THERAPEUTICS, INC.

(Name of Issuer)

Common Stock, $0.0001 par value

(Title of Class of Securities)

75382E 109

(CUSIP Number)

Peter Svennilson

The Column Group II, LP

1 Letterman Drive, Building D, Suite DM-900

San Francisco, CA 94129

(415) 865-2050

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

May 10, 2022

(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) or 240.13d-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. 75382E 109


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

(1)

The securities are directly held by The Column Group II, LP (“TCG II LP”). The Column Group II GP, LP (“TCG II GP”) is the general partner of TCG II LP and may be deemed to have voting and investment power with respect to these securities. The managing partners of TCG II GP are David Goeddel and Peter Svennilson (collectively, the “TCG II GP Managing Partners”). The TCG II GP Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)

This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its prospectus supplement filed with the Securities and Exchange Commission on November 18, 2022 (the “Prospectus Supplement”).

CUSIP No. 75382E 109


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

(1)

The securities are directly held by TCG II LP. TCG II GP is the general partner of TCG II LP and may be deemed to have voting and investment power with respect to these securities. The managing partners of TCG II GP are the TCG II GP Managing Partners. The TCG II GP Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


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

(1)

The securities are directly held by Ponoi Capital, LP (“Ponoi LP”). Ponoi Management, LLC (“Ponoi LLC”) is the general partner of Ponoi LP and may be deemed to have voting and investment power with respect to these securities. The managing partners of Ponoi LLC are the TCG II GP Managing Partners and Tim Kutzkey (collectively, the “Ponoi Managing Partners”). The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


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

(1)

The shares are directly held by Ponoi LP. Ponoi LLC is the general partner of Ponoi LP and may be deemed to have voting and investment power with respect to these shares. The managing partners of Ponoi LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person Ponoi Capital 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

(1)

The shares are directly held by Ponoi Capital II, LP (“Ponoi II LP”). Ponoi II Management, LLC (“Ponoi II LLC”) is the general partner of Ponoi II LP and may be deemed to have voting and investment power with respect to these shares. The managing partners of Ponoi II LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person Ponoi II 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

(1)

The shares are directly held by Ponoi II LP. Ponoi II LLC is the general partner of Ponoi II LP and may be deemed to have voting and investment power with respect to these shares. The managing partners of Ponoi II LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person The Column Group IV, 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 securities are directly held by The Column Group IV, LP (“TCG IV LP”). The Column Group IV GP, LP (“TCG IV GP”) is the general partner of TCG IV LP and may be deemed to have voting and investment power with respect to these securities. TCG IV GP LP is the general partner of TCG IV LP may be deemed to have voting, investment and dispositive power with respect to these securities. The Ponoi Managing Partners are the managing partners of TCG IV GP LP and may each be deemed to share voting, investment and dispositive power with respect to these securities.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person The Column Group IV-A, 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 securities are directly held by The Column Group IV-A, LP (“TCG IV-A LP”). TCG IV GP is the general partner of TCG IV-A LP and may be deemed to have voting and investment power with respect to these securities. TCG IV GP LP is the general partner of TCG IV-A LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The Ponoi Managing Partners are the managing partners of TCG IV GP LP and may each be deemed to share voting, investment and dispositive power with respect to these securities.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person The Column Group IV 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

(1)

Consists of (i) 1,236,261 shares are held of record by TCG IV LP and (ii) 42,189 shares held by TCG IV-A LP. TCG IV GP is the general partner of each of TCG IV LP and TCG IV-A LP and may be deemed to have voting and investment power with respect to these securities. TCG IV GP LP is the general partner of each of TCG IV LP and TCG IV-A LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The Ponoi Managing Partners are the managing partners of TCG IV GP LP and may each be deemed to share voting, investment and dispositive power with respect to these securities.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


1.		Name of Reporting Person The Column Group, 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

(1)	The shares are directly held The Column Group LLC (“TCG LLC”). The managing members of TCG LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to such shares.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


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

(1)

Consists of (i) 1,402,008 shares held directly by TCG II LP (ii) 1,599,417 shares held directly by Ponoi LP (iii) 145,401 shares held directly by Ponoi II LP, (iv) 1,236,261 shares held directly by TCG IV LP, (v) 42,189 shares held directly by TCG IV-A LP and (vi) 163 shares held directly by TCG LLC. TCG II GP is the general partner of TCG II LP and may be deemed to have voting and investment power with respect to the shares held by TCG II LP. The managing partners of TCG II GP are the TCG II GP Managing Partners. The TCG II GP Managing Partners may be deemed to share voting and investment power with respect to the shares held by TCG II LP. Ponoi LLC is the general partner of Ponoi LP and may be deemed to have voting and investment power with respect to the shares held by Ponoi LP. Ponoi II LLC is the general partner of Ponoi II LP and may be deemed to have voting and investment power with respect to the shares held by Ponoi LP. The managing partners of each of Ponoi LLC, Ponoi II LLC and TCG LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to the shares held by each of Ponoi LP, Ponoi II LP and TCG LLC. TCG IV GP LP is the general partner of each of TCG IV LP and TCG IV-A LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The Ponoi Managing Partners are the managing partners of TCG IV GP LP and may each be deemed to share voting, investment and dispositive power with respect to these securities.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


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.

(1)

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

CUSIP No. 75382E 109


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.

(1)

Consists of (i) 1,599,417 shares held directly by Ponoi LP (ii) 145,401 shares held directly by Ponoi II LP, (iii) 1,236,261 shares held directly by TCG IV LP, (iv) 42,189 shares held directly by TCG IV-A LP and (v) 163 shares held directly by TCG LLC. Ponoi LLC is the general partner of Ponoi LP and may be deemed to have voting and investment power with respect to the shares held by Ponoi LP. Ponoi II LLC is the general partner of Ponoi II LP and may be deemed to have voting and investment power with respect to the shares held by Ponoi LP. The managing partners of each of Ponoi LLC, Ponoi II LLC and TCG LLC are the Ponoi Managing Partners. The Ponoi Managing Partners may be deemed to share voting and investment power with respect to the shares held by each of Ponoi LP, Ponoi II LP and TCG LLC. TCG IV GP LP is the general partner of each of TCG IV LP and TCG IV-A LP and may be deemed to have voting, investment and dispositive power with respect to these securities. The Ponoi Managing Partners are the managing partners of TCG IV GP LP and may each be deemed to share voting, investment and dispositive power with respect to these securities.

(2)	This calculation is based upon 33,940,217 shares of Common Stock outstanding (assuming the underwriters do not exercise their option to purchase additional shares) as reported by the Issuer in its Prospectus Supplement.

SCHEDULE 13D

Explanatory Note:

This joint statement on Schedule 13D/A (this “Statement”) is being filed late due to an administrative error.

Item 1.

Security and Issuer

This Amendment No. 6 (“Amendment No. 6”) supplements and amends the Schedule 13D relating to shares of common stock, par value $0.0001 per share (the “Common Stock”), of RAPT Therapeutics, Inc., a Delaware corporation (the “Issuer”) that was filed with the Securities and Exchange Commission (the “SEC”) on November 8, 2019 as it was amended by Amendment No. 1 thereto filed with the SEC on February 14, 2020, Amendment No. 2 thereto filed with the SEC on August 26, 2020, Amendment No. 3 thereto filed with the SEC on October 1, 2020, Amendment No. 4 thereto filed with the SEC on August 30, 2021 and Amendment No. 5 thereto filed with the SEC on September 20, 2021 (collectively, the “Amended Statement”). Only those items that are reported are hereby amended; all other items reported in the Amended Statement remain unchanged. Capitalized terms contained herein but not otherwise defined shall have the meanings ascribed to such terms in the Amended Statement. Information given in response to each item shall be deemed incorporated by reference in all other items as applicable.

Item 5.

Interest in Securities of the Issuer

Solely on behalf of, and only to the extent that it relates to the Reporting Persons, Item 5 of the Amended Statement is hereby amended as follows:

(a) and (b) See Items 7-11 of the cover pages of this Amendment No. 6.

(c) On May 10, 2022, TCG IV LP purchased 1,208,750 Common Shares at a weighted average price per share of $10.6715 for aggregate purchase price of approximately $12,899,176.

On May 10, 2022, TCG IV-A LP purchased 41,250 Common Shares at a weighted average price per share of $10.6715 for aggregate purchase price of approximately $440,200.

On May 23, 2022, TCG IV LP purchased 9,898 Common Shares at a weighted average price per share of $12.4993 for aggregate purchase price of approximately $123,719.

On May 23, 2022, TCG IV-A LP purchased 338 Common Shares at a weighted average price per share of $12.4993 for aggregate purchase price of approximately $4,225.

On May 24, 2022, TCG IV LP purchased 15,776 Common Shares at a weighted average price per share of $12.0021 for aggregate purchase price of approximately $189,346.

On May 24, 2022, TCG IV-A LP purchased 538 Common Shares at a weighted average price per share of $12.0021 for aggregate purchase price of approximately $6,458.

On May 25, 2022, TCG IV LP purchased 1,837 Common Shares at a weighted average price per share of $12.4549 for aggregate purchase price of approximately $22,880.

On May 25, 2022, TCG IV-A LP purchased 63 Common Shares at a weighted average price per share of $12.4549 for aggregate purchase price of approximately $785.

(d) Under certain circumstances set forth in the respective limited partnership agreements of each of TCG II LP, TCG IV LP, TCG IV-A LP, Ponoi LP and Ponoi II LP (the “Funds”), the respective general partners and limited partners of the Funds may be deemed to have the right to receive dividends from, or the proceeds from, the sale of shares of the Issuer owned by such entity of which they are a partner.

(e) Not applicable.

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: January 13, 2023


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

By:	The Column Group II GP, LP	By:	/s/ James Evangelista, Attorney-in-Fact

By:	/s/ James Evangelista, Attorney-in-Fact

PONOI CAPITAL, LP		PONOI MANAGEMENT, LLC

By:	Ponoi Management, LLC	By:	/s/ James Evangelista, Attorney-in-Fact

By:	/s/ James Evangelista, Attorney-in-Fact

PONOI CAPITAL II, LP		PONOI II MANAGEMENT, LLC

By:	Ponoi II Management, LLC	By:	/s/ James Evangelista, Attorney-in-Fact

By:	/s/ James Evangelista, Attorney-in-Fact

THE COLUMN GROUP, LLC

By:	/s/ James Evangelista, Attorney-in-Fact

THE COLUMN GROUP IV, LP		THE COLUMN GROUP IV-A, LP

By:	The Column Group IV GP, LP	By:	The Column Group IV GP, LP

By:	/s/ James Evangelista, Attorney-in-Fact	By:	/s/ James Evangelista, Attorney-in-Fact

HE COLUMN GROUP IV GP, LP		TCG IV GP, LLC

By:	/s/ James Evangelista, Attorney-in-Fact		/s/ James Evangelista, Attorney-in-Fact

By:	/s/ James Evangelista, Attorney-in-Fact on behalf of Peter Svennilson	By:	/s/ James Evangelista, Attorney-in-Fact on behalf of Tim Kutzkey

By:	/s/ James Evangelista, Attorney-in-Fact on behalf of David V. Goeddel

Number of
Shares
Beneficially
by
Owned by
Each
Reporting
Person
With

Sole Voting Power:

1,402,008 (1)

Shared Voting Power:

0

Sole Dispositive Power:

1,402,008 (1)

Shared Dispositive Power:

0