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This Amendment No. 2 (the “Amendment”) amends and supplements the Statement on Schedule 13D, dated March 27, 2014 and filed on April 7, 2014, as amended by Amendment No. 1 dated December 31, 2014 and filed on January 5, 2015 (the “Original Schedule 13D”), relating to the Common Stock, no par value per share (the “Common Stock”), of Intrexon Corporation, a Virginia corporation (the “Company”). Mr. Randal J. Kirk (“Mr. Kirk”), Third Security, LLC, a Virginia limited liability company that is controlled by Mr. Kirk (“Third Security”), Kapital Joe, LLC, a Virginia limited liability company that is managed by Third Security (“Kapital Joe”), Mascara Kaboom, LLC, a Virginia limited liability company that is managed by Third Security (“Mascara Kaboom”), New River Management V, LP (“NRM V”), a Delaware limited partnership whose general partner is managed by Third Security, and NRM VI Holdings I, LLC, a Delaware limited liability company that is managed by an affiliate that is managed by Third Security (“NRM VI Holdings” and, together with Mr. Kirk, Third Security, Kapital Joe, Mascara Kaboom and NRM V, the “Reporting Persons”) are filing this Amendment to disclose the distribution of 1,196,077 shares of Common Stock in connection with the liquidation of New River Management IV, LP, a Virginia limited partnership whose general partner is managed by Third Security (“NRM IV”), at the end of its term, pursuant to its Agreement of Limited Partnership dated May 31, 2006 and amendments thereto. In connection with such liquidation, 705,379 of such shares are being distributed to entities under the common control of Mr. Kirk.

Item 4.

Purpose of Transaction.

Item 4 of the Original Schedule 13D is hereby amended and supplemented as follows:

The Reporting Persons are filing this Amendment to disclose the distribution of 1,196,077 shares of Common Stock in connection with the liquidation of NRM IV, at the end of its term, pursuant to its Agreement of Limited Partnership dated May 31, 2006 and amendments thereto. In connection with the liquidation, 705,379 of such shares are being distributed to entities under the common control of Mr. Kirk.

Item 5.

Interest in Securities of the Issuer.

Items 5(a) and (b) of the Original Schedule 13D are hereby amended and restated to read in their entirety as follows:

(a) and (b)           See items 11 and 13 of the cover pages to this Statement for the aggregate number of shares and percentage of issued and outstanding shares of Common Stock of the Company owned by the Reporting Persons. The percentage ownership is calculated based on 118,164,614 shares of Common Stock issued and outstanding as of April 30, 2016 as disclosed in the Intrexon Corporation Quarterly Report on Form 10-Q for the period ended March 31, 2016 and filed on May 10, 2016, increased by (i) options to purchase 11,828 shares of Common Stock held by Mr. Kirk that are exercisable within sixty (60) days, (ii) 32,854 shares of Common Stock issued to Third Security on May 31, 2016 pursuant to the Services Agreement by and between the Company and Third Security dated November 1, 2015 (the “Services Agreement”) and (iii) 6,506 shares of Common Stock issued to Randal J. Kirk on May 31, 2016 pursuant to the Restricted Stock Unit Agreement by and between the Company and Randal J. Kirk dated November 1, 2015 (the “RSU Agreement”) .

 

Mr. Kirk could be deemed to have indirect beneficial ownership of the shares of Common Stock directly beneficially owned by Third Security, Kapital Joe, Mascara Kaboom, NRM V and NRM VI Holdings. Mr. Kirk controls Third Security, which is the manager of Kapital Joe and Mascara Kaboom and which manages the general partner of NRM V and the manager of NRM VI Holdings.

(c)                 Pursuant to the Services Agreement, the Company will pay to Third Security, on a monthly basis, such number of shares of Common Stock, rounded down to the nearest whole number, equal to a value of $800,000. Pursuant to the Services Agreement, on April 29, 2016, the Company issued 21,074 shares of Common Stock to Third Security and on May 31, 2016, the Company issued 32,854 shares of Common Stock to Third Security.

Pursuant to the RSU Agreement, Mr. Kirk will receive, on a monthly basis, that number of shares of Common Stock, rounded down to the nearest whole share, whose fair market value equals $200,000. The number of shares of Common Stock are to become vested and payable based upon the closing price of the Common Stock on the New York Stock Exchange on the last calendar day of each month (or, if such date is not a trading day, the most recent trading day prior to such date). Pursuant to the RSU Agreement, on April 29, 2016, the Company issued 7,482 shares of Common Stock to Mr. Kirk and on May 31, 2016, the Company issued 6,506 shares of Common Stock to Mr. Kirk.

On May 13, 2016, Kapital Joe purchased 41,830 shares of Common Stock in the open market.

(d) – (e)

Not applicable

Item 6.

Contracts, Arrangements, Understandings or Relationships with Respect to Securities of the Issuer.

The Reporting Persons’ responses to Items 4 and 5 are incorporated herein by reference.

 

Item 7.

Material to be Filed as Exhibits.

Exhibit 1

Services Agreement, dated as of November 1, 2015, by and among Third Security, LLC and Intrexon Corporation (filed as Exhibit 10.1 to the Current Report on Form 8-K/A dated October 30, 2015 and filed on November 3, 2015, and incorporated herein by reference).

Exhibit 2

Restricted Stock Unit Agreement, dated as of November 1, 2015, by and among Randal J. Kirk and Intrexon Corporation (filed as Exhibit 10.2 to the Current Report on Form 8-K/A dated October 30, 2015 and filed on November 3, 2015, and incorporated herein by reference).

Exhibit 3

Joint Filing Agreement, dated as of June 2, 2016, by and among Randal J. Kirk, Third Security, LLC, Kapital Joe, LLC, Mascara Kaboom, LLC, New River Management V, LP and NRM VI Holdings I, LLC.

 

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

Date: June 2, 2016

 

Exhibit 1

Services Agreement, dated as of November 1, 2015, by and among Third Security, LLC and Intrexon Corporation (filed as Exhibit 10.1 to the Current Report on Form 8-K/A dated October 30, 2015 and filed on November 3, 2015, and incorporated herein by reference).

Exhibit 2

Restricted Stock Unit Agreement, dated as of November 1, 2015, by and among Randal J. Kirk and Intrexon Corporation (filed as Exhibit 10.2 to the Current Report on Form 8-K/A dated October 30, 2015 and filed on November 3, 2015, and incorporated herein by reference).

Exhibit 3

Joint Filing Agreement, dated as of June 2, 2016, by and among Randal J. Kirk, Third Security, LLC, Kapital Joe, LLC, Mascara Kaboom, LLC, New River Management V, LP and NRM VI Holdings I, LLC.

 

 

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