13D Filing: Alafi Capital Co LLC and Intra-Cellular Therapies Inc. (ITCI)

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, DC 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)

INTRA-CELLULAR THERAPIES, INC.

(Name of Issuer)

Common
Stock, par value $0.0001 per share

(Title of Class of Securities)

46116X 101

(CUSIP
Number)

Intra-Cellular Therapies, Inc.

430 East 29^th Street

New York, NY 10016

Telephone: (646) 440-9333

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

October 2, 2017

(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 Rule
13d-7 for other parties to whom copies are to be sent.

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).

This Schedule 13D relates to the common stock, par value $0.0001
per share (the Common Stock) of Intra-Cellular Therapies, Inc., a Delaware corporation (Intra-Cellular or the Issuer). Intra-Cellulars principal executive offices are located at 430 East 29^th Street, New York, NY 10016.

Alafi Capital Company, LLC

(a) This Schedule 13D is being filed on behalf of Alafi Capital Company, LLC, a California limited liability company (Alafi
Capital, and together with Christopher Alafi, Ph.D. and Moshe Alafi, the Reporting Persons).

(b) The business address
of Alafi Capital is 8 Admiral Drive, Suite 324, Emeryville, CA 94608.

(c) The principal business of Alafi Capital is to invest in
healthcare companies.

(d) During the past five years, Alafi Capital has not been convicted in any criminal proceeding (excluding traffic
violations or similar misdemeanors).

(e) During the past five years, Alafi Capital has not been a party to a civil proceeding of a
judicial or administrative body of competent jurisdiction where as a result of such proceeding it was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or
state securities laws or finding any violation with respect to such laws.

(f) Not applicable.

Christopher Alafi, Ph.D.

(a) This Schedule 13D is being filed on behalf of Christopher Alafi, Ph.D.

(b) The business address of Dr. Alafi is c/o Alafi Capital Company, LLC, 8 Admiral Drive, Suite 324, Emeryville, CA 94608.

(c) Dr. Alafi is a managing partner of Alafi Capital Company, LLC, whose principal business is to invest in healthcare companies. In
addition, Dr. Alafi is a member of the board of directors of Intra-Cellular.

(d) During the past five years, Dr. Alafi has not
been convicted in any criminal proceeding (excluding traffic violations or similar misdemeanors).

(e) During the past five years,
Dr. Alafi has not been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction where as a result of such proceeding he was or is subject to a judgment, decree or final order enjoining future violations of,
or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws.

(f) Dr. Alafi is a citizen of the United States.

Moshe Alafi

(a) This
Schedule 13D is being filed on behalf of Moshe Alafi.

(b) The business address of Moshe Alafi is c/o Alafi Capital Company, LLC, 8
Admiral Drive, Suite 324, Emeryville, CA 94608.

(c) Moshe Alafi is a managing partner of Alafi Capital Company, LLC, whose principal
business is to invest in healthcare companies.

(d) During the past five years, Moshe Alafi has not been convicted in any criminal proceeding
(excluding traffic violations or similar misdemeanors).

(e) During the past five years, Moshe Alafi has not been a party to a civil
proceeding of a judicial or administrative body of competent jurisdiction where as a result of such proceeding he was or is subject to a judgment, decree or final order enjoining future violations of, or prohibiting or mandating activities subject
to, federal or state securities laws or finding any violation with respect to such laws.

(f) Moshe Alafi is a citizen of the United
States.

The sources of funds used by the
Reporting Persons to purchase the Issuers securities have been personal funds with respect to purchases by Dr. Alafi and Mr. Alafi and capital contributions from members of Alafi Capital with respect to purchases by Alafi Capital.

The information contained in Item 4 is incorporated herein by reference.

Private Placement

Prior to the Merger (defined below), Intra-Cellular Therapies, Inc., a private Delaware corporation (ITI), sold to accredited
investors approximately $60.0 million of its shares of common stock, or 18,889,307 shares at a price of $3.1764 per share, which included approximately $15.3 million in principal and $0.8 million in accrued interest from the conversion of ITIs
then outstanding convertible promissory notes (the Private Placement).

Also, ITI granted the investors in the Private
Placement, and the other then existing stockholders of ITI, registration rights requiring ITI or any successor to register those shares of ITIs common stock (which were exchanged for shares of the Issuers Common Stock in the Merger) for
public resale, as described in more detail below. The Private Placement closed immediately prior to the Merger on August 29, 2013.

Alafi Capital purchased 3,619,234 shares of ITIs common stock in the Private Placement for a purchase price of $11,496,135, including
$6,748,637 in principal and accrued interest from the conversion of a then outstanding convertible promissory note of ITI originally issued to Alafi Capital on October 25, 2012.

Moshe Alafi purchased 31,484 shares of ITIs common stock in the Private Placement for a purchase price of $100,006.

Christopher Alafi, Ph.D. did not purchase shares in the Private Placement.

Reverse Merger

Pursuant to an
Agreement and Plan of Merger dated August 23, 2013 (the Merger Agreement) by and among the Issuer, ITI, Inc., a Delaware corporation and wholly-owned subsidiary of the Issuer (Merger Sub), and ITI, Merger Sub merged with
and into ITI, with ITI remaining as the surviving entity and a wholly-owned operating subsidiary of the Issuer (the Merger). The Merger was effective as of August 29, 2013 (the Effective Time). As part of the Merger, ITI
changed its name to ITI, Inc.

At the Effective Time, the legal existence of Merger Sub ceased and each share of ITIs common stock
and each share of ITIs preferred stock that was issued and outstanding immediately prior to the Effective Time was automatically exchanged for 0.5 shares of the Issuers Common Stock. The Issuer issued an aggregate of 22,134,647 shares of
its Common Stock upon such exchange.

Following the Merger, effective on August 29, 2013, a newly organized wholly-owned subsidiary
of the Issuer named Intra-Cellular Therapies, Inc. merged with and into the Issuer, leaving the Issuer as the surviving corporation. In connection with this merger, the Issuer, which was formerly named Oneida Resources Corp., assumed the
name Intra-Cellular Therapies, Inc.

In addition, at the Effective Time, the Issuer assumed ITIs 2003 Equity Incentive Plan,
as amended, (the 2003 Equity Incentive Plan), and all options to purchase ITIs common stock then outstanding under the 2003 Equity Incentive Plan, and such options became exercisable for an aggregate of 1,462,380 shares of the
Issuers Common Stock, subject to the vesting and other terms of such options. The vesting of such options was not accelerated as a result of the Merger. At the Effective Time, the Issuer also assumed a warrant to purchase ITIs common
stock, and such warrant became exercisable for 1,822 shares of the Issuers Common Stock.

Upon the effectiveness of the Merger, the
Issuers business became the operation of ITI and its business. Immediately following the Effective Time, the Issuers Board of Directors (the Board), which immediately prior to the Effective Time consisted of Samir N. Masri as
the Issuers sole director, appointed Sharon Mates, Ph.D., who was Chairman, President and Chief Executive Officer of ITI, as the Issuers Chairman, President and Chief Executive Officer, to serve on the Board with Mr. Masri. At the
Effective Time, Mr. Masri resigned from all of his positions as an officer of the Issuer. In addition, immediately following the Effective Time, the Board appointed Lawrence J. Hineline, who was the Vice President of Finance, Chief Financial
Officer and Secretary of ITI, as the Issuers Vice President of Finance, Chief Financial Officer and Secretary; Allen A. Fienberg, Ph.D., who was the Vice President of Business Development of ITI, as the Issuers Vice President of Business
Development; Lawrence P. Wennogle, Ph.D., who was the Vice President, Drug Discovery of ITI, as the Issuers Vice President, Drug Discovery; and Kimberly E. Vanover, Ph.D., who was the Vice President, Clinical Development of ITI, as the
Issuers Vice President, Clinical Development. On September 9, 2013, which is the eleventh day following the date that the Issuer filed with SEC, and transmitted to the Issuers sole stockholder prior to the Merger, a Schedule 14f-1
reporting a change in the majority of the Issuers directors, Christopher Alafi, Ph.D., Richard Lerner, M.D., Joel S. Marcus and Sir Michael Rawlins, M.D., FRCP, FMedSci, were appointed to the Board to serve on the Board with Dr. Mates,
and Mr. Masri resigned from the Board as of such date. Each of Dr. Mates, Dr. Alafi, Dr. Lerner, Mr. Marcus, and Sir Michael were directors of ITI immediately prior to the Merger.

Immediately following the Effective Time, the Issuer redeemed all shares of its capital stock issued and outstanding immediately prior to the
Merger. Upon completion of the Merger and this redemption, the former stockholders of ITI held 100% of the outstanding shares of the Issuers capital stock.

Immediately prior to the consummation of the Merger, Alafi Capital owned 3,619,234 shares of ITIs common stock purchased in the Private
Placement and 3,466,535 shares of ITIs preferred stock, which were exchanged for an aggregate of 3,542,885 shares of the Issuers Common Stock upon the consummation of the Merger. Alafi Capital purchased the 3,466,535 shares of ITIs
preferred stock held by Alafi Capital immediately prior to the Merger in ITIs preferred stock financings in May 2002, January 2006, October 2007 and February 2010.

Immediately prior to the consummation of the Merger, Christopher Alafi, Ph.D. beneficially owned 1,007,505 shares of ITIs preferred
stock held by a trust for the benefit of members of the Alafi family, which were exchanged for an aggregate of 503,753 shares of the Issuers Common Stock upon the consummation of the
Merger.¹² These 1,007,505 shares of ITIs preferred stock were originally purchased from ITI by Alafi Capital in February 2010 and were subsequently transferred to the trust in December 2012.
In addition, upon the consummation of the Merger, the Issuer assumed options held by Dr. Alafi to purchase 29,375 shares of the Issuers Common Stock.

Immediately prior to the consummation of the Merger, Moshe Alafi owned 31,484 shares of ITIs common stock, which he purchased in the
Private Placement, and which were exchanged for an aggregate of 15,742 shares of the Issuers Common Stock upon the consummation of the Merger.¹³

Effective August 29, 2013, prior to the Merger, the Issuers sole director and sole stockholder approved by written consent a
restated certificate of incorporation to, among other things, reduce the number of authorized shares of preferred stock, provide for the Issuers Board of Directors to be divided into three classes, require that any action

taken by the Issuers stockholders be at a duly called annual or special meeting of stockholders and not by written consent, and to require a supermajority vote of the Issuers
stockholders for the Issuers stockholders to remove any of the Issuers directors, amend, alter or repeal, or adopt any provision inconsistent with, certain provisions contained in the Issuers restated certificate of incorporation,
or to adopt, amend or repeal the Issuers restated bylaws. The restated certificate of incorporation became effective on November 7, 2013. Under the restated certificate of incorporation, the Issuer has authorized capital stock of
105,000,000 shares, of which 100,000,000 shares is designated as Common Stock, and of which 5,000,000 shares is designated as preferred stock, par value $0.0001 per share.

Effective August 29, 2013, the Issuers sole director approved the Issuers restated bylaws to, among other things, provide for
the Board of Directors to be divided into three classes, require that any action taken by the Issuers stockholders be at a duly called annual or special meeting of stockholders and not by written consent, and to require a supermajority vote of
the Issuers stockholders for the Issuers stockholders to remove any of the Issuers directors or to adopt, amend or repeal any provision of the Issuers restated bylaws.

Purchases and Sales of Common Stock

On June 19, 2014, Moshe Alafi sold 15,742 shares of Common Stock to a family member of Mr. Alafi at a price per share equal to the
price at which Mr. Alafi originally purchased shares of ITI, Inc. common stock in the Private Placement, as adjusted for the exchange for shares of the Issuers Common Stock in the Merger, or $6.3528 per share.

Alafi Capital purchased 5,000 shares of Common Stock on the open market at $15.55 per share on November 11, 2014, 5,000 shares of Common
Stock on the open market at $15.23 per share on November 12, 2014, 2,200 shares of Common Stock on the open market at $15.12 per share on November 13, 2014, 133 shares of Common Stock on the open market at $15.07 per share on
November 14, 2014, 3,531 shares of Common Stock on the open market at $14.23 per share on November 18, 2014, 1,034 shares of Common Stock on the open market at $14.25 per share on November 19, 2014, 35,000 shares of Common Stock on
the open market at $14.75 per share on November 28, 2014, 1,422 shares of Common Stock on the open market at $14.75 per share on December 1, 2014, 34,000 shares of Common Stock on the open market at $14.4991 per share on November 14, 2016,
44,174 shares of Common Stock on the open market at $16.3319 per share on December 6, 2016 and 20,826 shares of Common Stock on the open market at $16.1355 per share on December 7, 2016.

Christopher Alafi, Ph.D. purchased 100,000 shares of Common Stock on the open market at $29.703 per share on February 29, 2016.

Purchases of Common Stock in the Issuers March 2015 Public Offering

On March 11, 2015, Dr. Alafi acquired 625,000 shares of Common Stock in the Issuers public offering at the public offering
price of $24.00 per share. Dr. Alafi acquired the Issuers securities in the public offering for investment purposes.

September 2015
Public Offering

On September 28, 2015, the Issuer closed a public offering in which the Issuer sold 7,935,000 shares of Common
Stock. None of the Reporting Persons purchased any shares of Common Stock in the offering. As a result of the offering, the percentage of the outstanding shares of Common Stock beneficially owned by the Reporting Persons decreased by more than 1%.

Purchases of Common Stock in the Issuers 2017 Public Offering

On October 2, 2017, Alafi Capital purchased 258,065 shares of Common Stock in the Issuers public offering at the public offering price of
$15.50 per share. Alafi Capital acquired the Issuers securities in the public offering for investment purposes.

Stock Grants Pursuant to the
Issuers Non-Employee Director Compensation Policy

In accordance with the Issuers Non-Employee Director Compensation
Policy, as compensation for Dr. Alafis role as a director of the Issuer, the Issuers Board of Directors granted Dr. Alafi the following number of shares of common stock on the following dates:

Stock Options Granted Pursuant to the Issuers Non-Employee Director Compensation Policy

As of October 5, 2017, Dr. Alafi holds (1) fully-vested options to purchase an aggregate of 89,375 shares of Common Stock and (2) an option to
purchase 20,000 shares of Common Stock, which vests on June 27, 2018.

Subject to applicable legal requirements, one or more of the
Reporting Persons may purchase additional securities of the Issuer from time to time in open market or private transactions, depending on their evaluation of the Issuers business, prospects and financial condition, the market for the
Issuers securities, other developments concerning the Issuer, the reaction of the Issuer to the Reporting Persons ownership of the Issuers securities, other opportunities available to the Reporting Persons and general economic,
money market and stock market conditions. In addition, depending upon the factors referred to above, the Reporting Persons may dispose of all or a portion of their securities of the Issuer at any time. Each of the Reporting Persons reserves the
right to increase or decrease its holdings on such terms and at such times as each may decide.

Other than as described in this
Item 4 or consistent with the rights of the Reporting Persons set forth in the Lock-up Agreements, as defined in Item 6 of this Statement, none of the Reporting Persons has any plans or proposals that relate to or would result in:
(a) the acquisition by any person of additional securities of the Issuer, or the disposition of securities of the Issuer; (b) an extraordinary corporate transaction, such as a merger, reorganization or liquidation, involving the Issuer or
any of its subsidiaries; (c) a sale or transfer of a material amount of assets of the Issuer or any of its subsidiaries; (d) any change in the present board of directors or management of the Issuer, including any plans or proposals to
change the number or term of directors or to fill any

existing vacancies on the board; (e) any material change in the present capitalization or dividend policy of the Issuer; (f) any other material change in the Issuers business or
corporate structure; (g) changes in the Issuers charter, by-laws or instruments corresponding thereto or other actions which may impede the acquisition of control of the Issuer by any person; (h) causing a class of securities of the
Issuer to be delisted from a national securities exchange or to cease to be authorized to be quoted in an inter-dealer quotation system of a registered national securities association; (i) a class of equity securities of the Issuer becoming
eligible for termination of registration pursuant to Section 12(g)(4) of the Act; or (j) any action similar to any of those enumerated above.

(a)-(b):

Number of shares of Common Stock beneficially owned:

Percent of class: (The percentage ownership was calculated based on 54,553,353 shares of Common Stock outstanding as of
October 5, 2017).

Number of shares as to which such person has:

(c) Except as set forth in Item 4 of this Schedule 13D, the Reporting Persons have not effected any
transactions with respect to the shares of the Common Stock during the past 60 days.

(d) Not applicable.

(e) Not applicable.

The information contained in Item 4 is incorporated herein by reference.

Registration Rights Agreement

At
the closing of the Private Placement, ITI entered into a registration rights agreement with the investors in the Private Placement (including Alafi Capital and Moshe Alafi) and also the existing stockholders of ITI who agreed to become parties to
certain provisions of the agreement (including Dr. Alafi) or who may choose to become parties in the future. The Issuer assumed the registration rights agreement in connection with the Merger. Pursuant to the registration rights agreement and
subject to the rules and regulations of the SEC, the Issuer agreed to file a shelf registration statement covering the resale of the shares of its Common Stock held by the investors in the Private Placement and the shares of the Issuers common
stock held by the former stockholders of ITI who are parties to the agreement. In accordance with the registration rights agreement, the Issuer filed a shelf registration statement on Form S-1 on September 18, 2013, which was initially declared
effective by the Securities and Exchange Commission on December 18, 2013.

The registration rights agreement provided that the Issuer
will be liable to each investor in the Private Placement (but not to the former stockholders of ITI who are parties to the agreement) for liquidated damages, on a 30-day basis, equal to 1.0% of the aggregate purchase price paid by the investor for
the registrable shares of the Issuers Common Stock then held by the investor, subject to an overall cap of 5%, (i) if the Issuer failed to file the registration statement on time, (ii) if the registration statement was not declared
effective within 150 days from the date of the registration rights agreement (January 26, 2014), (iii) if the Issuer suspended (subject to limited blackout periods described below) or terminates the registration statement prior to the date
which is the earlier of (x) the third anniversary of its effectiveness (or the third anniversary of the date on which all registrable shares are included therein, if later) and (y) the date on which all of the registrable shares cease to
be registrable shares, or (iv) in the event one or more suspensions of the effectiveness of the registration statement exceeds 60 days in the aggregate during any 12-month period. The Issuer filed a post-effective amendment to the shelf
registration statement on Form S-3 on May 14, 2014, which was declared effective by the Securities and Exchange Commission on May 16, 2014. The registration rights agreement provided that expenses with respect to the filing and
effectiveness of such registration statement (but not selling expenses, or underwriter or agent compensation) will be paid by the Issuer, including expenses of one counsel for the selling stockholders.

Lock-Up Agreement in Underwriting Agreement

The Underwriting Agreement by and among the Issuer and the Underwriters (as defined therein) dated September 27, 2017 contains a lock-up
agreement applicable to the certain stockholders of the Issuer (including Alafi Capital, Dr. Alafi, a trust for the benefit of Dr. Alafis family, and Moshe Alafi). Pursuant to the lock-up agreements,

these stockholders agreed, subject to specified exceptions, not to (i) offer, pledge, sell, contract to sell, sell any option or contract to purchase, purchase any option or contract to
sell, grant any option, right or warrant to purchase, or otherwise transfer or dispose of, directly or indirectly, any shares of Common Stock or any securities convertible into or exercisable or exchangeable for Common Stock, or publicly disclose
the intention to make any offer, sale, pledge or disposition, (ii) enter into any swap or other agreement that transfers, in whole or in part, any of the economic consequences of ownership of the Common Stock or such other securities, or
(iii) make any demand for or exercise any right with respect to the registration of any shares of Common Stock or any security convertible into or exercisable or exchangeable for Common Stock, without the prior written consent of J.P. Morgan
Securities LLC during the period ending 60 days after the date of the final prospectus relating to the public offering, which date is November 27, 2017.

These lock-up provisions will not apply to, among other things, shares of Common Stock acquired in open market transactions, or upon the
exercise of stock options granted pursuant to the Issuers equity incentive plans, so long as the shares acquired upon exercise remain subject to the lock-up provisions in the agreement, or certain gifts and other transfers for estate-planning
purposes or by stockholders who are entities to their limited or general partners, members or stockholders, as specified in the agreement.

The foregoing descriptions of the Merger Agreement, the Registration Rights Agreement and the Lock-Up Agreement in the Underwriting Agreement
do not purport to be complete and are qualified in their entirety by reference to such agreements, which are attached hereto as Exhibits 2, 3 and 4, respectively, and are incorporated herein by reference.

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.