Sec Form 13D Filing - COLUMN GROUP II LP filing for RAPT THERAPEUTICS INC (RAPT) - 2023-01-13

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.

  Name of Reporting Person

  The Column Group II, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  WC

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

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

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,402,008 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  4.1% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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”).

  Name of Reporting Person

  The Column Group II GP, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  1,402,008 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  1,402,008 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,402,008 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  4.1% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  Ponoi Capital, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  WC

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  1,599,417 (1)

  Shared Voting Power:

  0

  Sole Dispositive Power:

  1,599,417 (1)

  Shared Dispositive Power:

  0

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,599,417 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  4.7% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  Ponoi Management, LLC

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  1,599,417 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  1,599,417 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,599,417 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amoun t in Row (11):

  4.7% (2)

  Type of Reporting Person (See Instructions):

  OO

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.

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.

  Name of Reporting Person

  Ponoi Capital II, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  WC

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  145,401 (1)

  Shared Voting Power:

  0

  Sole Dispositive Power:

  145,401 (1)

  Shared Dispositive Power:

  0

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  145,401 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  0.4% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  Ponoi II Management, LLC

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  145,401 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  145,401 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  145,401 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  0.4% (2)

  Type of Reporting Person (See Instructions):

  OO

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.

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.

  Name of Reporting Person

  The Column Group IV, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  WC

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  1,236,261 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  1,236,261 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,236,261 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  3.6% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  The Column Group IV-A, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  WC

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  42,189 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  42,189 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  42,189 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  0.1% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  The Column Group IV GP, LP

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  1,278,450 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  1,278,450 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  1,278,450 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  3.8% (2)

  Type of Reporting Person (See Instructions):

  PN

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.

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.

  Name of Reporting Person

  The Column Group, LLC

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Delaware

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  163 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  163 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  163 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  0.0% (2)

  Type of Reporting Person (See Instructions):

  OO

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.

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.

  Name of Reporting Person

  Peter Svennilson

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  Sweden

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  Shared Voting Power:

  4,425,439 (1)

  Sole Dispositive Power:

  Shared Dispositive Power:

  4,425,439 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  4,425,439 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  13.1% (2)

  Type of Reporting Person (See Instructions):

  IN

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.

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.

  Name of Reporting Person

  David V. Goeddel

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  U.S.A.

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  4,425,439 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  4,425,439 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  4,425,439 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  13.1% (2)

  Type of Reporting Person (See Instructions):

  IN

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.

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.

  Name of Reporting Person

  Tim Kutzkey

  Check the Appropriate Box if a Member of a Group (See Instructions)

  (a)  ☐        (b)  ☒

  SEC Use Only:

  Source of Funds (See Instructions):

  AF

  Check if Disclosure of Legal Proceedings Is Required Pursuant to Items 2(d) or 2(e):

  ☐

  Citizenship or Place of Organization:

  U.S.A.

Number of

Shares

 Beneficially 

by

Owned by

Each

Reporting

Person

With

  Sole Voting Power:

  0

  Shared Voting Power:

  3,023,431 (1)

  Sole Dispositive Power:

  0

  Shared Dispositive Power:

  3,023,431 (1)

  Aggregate Amount Beneficially Owned by Each Reporting Person:

  3,023,431 (1)

  Check if the Aggregate Amount in Row (11) Excludes Certain Shares (See Instructions):

  ☐

  Percent of Class Represented by Amount in Row (11):

  8.9% (2)

  Type of Reporting Person (See Instructions):

  IN

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.

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.

Security and Issuer

Interest in Securities of the Issuer

Dated: January 13, 2023

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact

/s/ James Evangelista, Attorney-in-Fact on behalf
of Peter Svennilson

/s/ James Evangelista, Attorney-in-Fact on behalf
of Tim Kutzkey

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