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                                                                     Exhibit 4.9

                             STOCK PURCHASE WARRANT

                                     For the purchase of up to 534,397 shares of
                                           Series E Convertible Preferred Stock,
                                                       par value $.001 per share

No. W-TCC-01E                                                  December 19, 2003

PTC Therapeutics, Inc., a Delaware corporation (the "Company"), hereby certifies
that, for good and valuable consideration, Three Crowns Capital (Bermuda) Ltd.
or its permitted assigns (the "Warrant Holder") is entitled, subject to the
terms set forth below, to purchase from the Company at any time on or before
5:00 p.m., Boston, Massachusetts time, on December 19, 2013 (the "Exercise
Period"), up to 534,397 fully-paid and non-assessable shares of Series E
Convertible Preferred Stock, par value $.001 per share, of the Company (the
"Series E Preferred Stock"), or shares of the Common Stock, par value $.001 per
share, of the Company (the "Common Stock") upon a mandatory conversion of the
Series E Preferred Stock as provided in Section 3 hereof (the Series E Preferred
Stock and the Common Stock are hereinafter collectively referred to as
"Shares"), at a price per share (the "Exercise Price") which shall initially be
$0.397644 per share and which shall be subject to adjustment as herein provided.

     1. Exercise of Warrants.

     1.1. Exercise. Subject to the terms and conditions of this Warrant, this
Warrant shall become exercisable by the Warrant Holder on December 19, 2003.

     1.2. Procedure to Exercise. This Warrant may be exercised by the Warrant
Holder, in whole or in part, by surrendering this Warrant, with the purchase
form appended hereto as Exhibit A duly executed by such Warrant Holder or by
such Warrant Holder's duly authorized attorney, at the principal office of the
Company, or at such other office or agency as the Company may designate,
accompanied by payment in full by cash, check or wire transfer of the amount
obtained by multiplying the number of Shares in the notice of exercise by the
Exercise Price (the "Purchase Price").

     1.3. Net Issue Exercise. In lieu of exercising this Warrant in the manner
provided above in Section 1.2, the Warrant Holder may elect to receive shares
equal to the value of this Warrant (or the portion thereof being converted) by
surrender of this Warrant, in whole or in part, at the principal office of the
Company together with the notice of exercise attached hereto as Exhibit A, in
which event the Company shall issue to the Warrant Holder the number of Shares
computed using the following formula (a "Net Issue Exercise"):

                                  X = Y (A - B)
                                      ---------
                                          A

Where: X = The number of Shares to be issued to the Warrant Holder.

       Y = The number of Shares purchasable under this Warrant (at the date of


                                      A-1

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              such calculation) that are being converted, in whole or in part,
              hereunder.

          A = The Fair Market Value of one Share (at the date of such
              calculation).

          B = The Exercise Price (as adjusted to the date of such calculation).

     For purposes of this Section 1.3, if any Shares of the Warrant Holder or
any other shareholder of the Company are registered or publicly traded, then the
Fair Market Value of one Share shall mean the average of the closing bid and
asked prices of the Common Stock quoted in the over the counter market summary
or the closing price quoted by the Nasdaq National Market or any exchange on
which the Common Stock is listed, whichever is applicable, as published in the
Western Edition of The Wall Street Journal (or the Financial Times (US Edition)
if not published in The Wall Street Journal) for the business day prior to the
date of determination of fair market value. If the Shares are not traded on the
Nasdaq National Market or on an exchange, the Fair Market Value of one Share
shall be determined in good faith by the Company's Board of Directors.

     1.4. Effectiveness. Each exercise or Net Issue Exercise of this Warrant
shall be deemed to have been effected immediately prior to the close of business
on the day on which this Warrant shall have been surrendered to the Company as
provided in Sections 1.2 or 1.3 above. At such time, the person or persons in
whose name or names any certificates for the Shares shall be issuable upon such
exercise or Net Issue Exercise as provided in Section 2 below shall be deemed to
have become the holder or holders of record of the Shares represented by such
certificates.

     2. Delivery of Stock Certificates, Etc. As soon as practicable after the
exercise or Net Issue Exercise of this Warrant in full or in part, and in any
event within 10 days thereafter, the Company at its expense will cause to be
issued in the name of, and delivered to, the Warrant Holder, or as such Warrant
Holder (upon payment by such Warrant Holder of any applicable transfer taxes)
may direct (i) a certificate or certificates for the number of fully paid and
non-assessable Shares to which the Warrant Holder shall be entitled upon such
exercise or Net Issue Exercise, and (ii) in case such exercise or Net Issue
Exercise is in part only, a new warrant or warrants (dated the date hereof) of
like tenor, calling in the aggregate on the face or faces thereof for the number
of Shares equal (without giving effect to any adjustment therein) to the number
of Shares called for on the face of this Warrant minus the number of Shares
purchased by the Warrant Holder upon such exercise or Net Issuance Exercise as
provided in Sections 1.2 or 1.3 herein.

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     3. Adjustments Upon Mandatory Conversion of Series E Preferred Stock. Upon
any mandatory conversion of the Series E Preferred Stock pursuant to the
Company's Certificate of Incorporation, as amended or amended and restated from
time to time, this Warrant shall cease to be exercisable for shares of Series E
Preferred Stock and shall become exercisable for that number of shares of Common
Stock into which the shares of Series E Preferred Stock purchasable hereunder
would have been convertible immediately prior to such mandatory conversion, and
such that payment of the Exercise Price, or any multiple thereof, shall entitle
the Warrant Holder to receive the number of shares of Common Stock as would have
been issued upon conversion of each share of Series E Preferred Stock
purchasable hereunder immediately prior to such mandatory conversion.

     4. Stock Splits, Stock Dividends and Combinations. If the Company at any
time subdivides the outstanding shares of Series E Preferred Stock, or issues a
stock dividend on the outstanding shares of Series E Preferred Stock, the
Exercise Price in effect immediately prior to such subdivision or the issuance
of such stock dividend shall be proportionately decreased, and the number of
Shares shall be proportionately increased, and if the Company at any time
combines the outstanding shares of Series E Preferred Stock, the Exercise Price
in effect immediately prior to such combination shall be proportionately
increased, and the number of shares shall be proportionately decreased,
effective at the close of business on the date of such subdivision, stock
dividend or combination, as the case may be. Upon any mandatory conversion of
the Series E Preferred Stock as provided in Section 3, each reference to Series
E Preferred Stock in this Section 4 shall be deemed to be Common Stock.

     5. Conversions; Reorganizations; Reclassifications; Merger; Sales. In case
of any capital reorganization or any reclassification of the capital stock of
the Company or in case of the consolidation or merger of the Company with or
into another corporation or the conveyance of all or substantially all of the
assets of the Company to another corporation (an "M&A Transaction"), this
Warrant shall thereafter be exercisable for the number of shares of stock or
other securities or property to which a holder of the number of Shares
deliverable upon exercise of the Warrant would have been entitled to upon such
conversion, reorganization, reclassification, consolidation, merger or
conveyance and, in any such case, appropriate adjustment as determined by the
Board of Directors of the Company shall be made in the application of the
provisions herein set forth with respect to the rights and interests thereafter
of the Warrant Holder to the end that the provisions set forth herein (including
provisions with respect to changes in and other adjustments of the Exercise
Price and the number of Shares) shall thereafter be applicable, as nearly as
reasonably may be, in relation to any shares of stock or other property
thereafter deliverable upon the exercise of the Warrant. Should the Board of
Directors make a good faith determination that compliance with the terms of this
Section will have a material adverse effect on the M&A Transaction, then the
Company may require that Warrant Holder exercise all or part of this Warrant on
the terms set forth herein.

     6. Statement of Adjustment. Whenever the Exercise Price shall be adjusted
as provided herein, the Company shall promptly file with the Secretary of the
Company or at such other place as shall be designated by the Company, a
statement, signed by its chief financial officer, showing in detail the facts
requiring such adjustment, the Exercise Price in effect before and after such
adjustment and the kind and amount of shares of capital stock, securities or
other property thereafter to be received upon the exercise of this Warrant. The
Company shall also

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cause a copy of such statement to be sent in the manner specified in Section
16.3 to the Warrant Holder.

     7. Notice of Adjustment. In the event the Company shall propose to take any
action of the types described in Sections 4 or 5, the Company shall give notice
to the Warrant Holder in the manner set forth in Section 16.3, which notice
shall specify the record date, if any, with respect to any such action and the
date on which such action is to take place. Such notice shall also set forth
such facts with respect thereto as shall be reasonably necessary to indicate the
effect of such action (to the extent such effect may be known at the date of
such notice) on the Exercise Price and the number, kind or class of shares or
other securities or property which shall be deliverable or purchasable upon the
occurrence of such action or deliverable upon the exercise hereof. In the case
of any action which would require the fixing of a record date, such notice shall
be given at least ten (10) days prior to the date so fixed, and in case of all
other actions, such notice shall be given at least twenty (20) days prior to the
taking of such proposed action. Failure to give such notice, or any defect
therein, shall not affect the legality or validity of any such action.

     8. Taxes. The Company shall pay all documentary, stamp or other
transactional taxes attributable to the issuance or delivery of shares of
capital stock of the Company upon the exercise or conversion hereof; provided,
however, Company shall have no obligation to pay any documentary, stamp or other
transactional taxes on transfers initiated by Warrant Holder.

     9. No Fractional Shares. Each adjustment in the number of Shares
purchasable hereunder shall be calculated, to the nearest whole share with
fractional shares disregarded.

     10. Covenants as to Series Preferred Stock and Common Stock. The Company
covenants and agrees that the shares of Series E Preferred Stock issuable
hereunder, and the Common Stock issuable upon conversion thereof, and the Common
Stock issuable hereunder, as the case may be, will, upon issuance in accordance
with the terms hereof, be validly issued and outstanding, fully paid and
nonassessable, and free from all taxes, liens and charges with respect to the
issuance thereof imposed by or through the Company. The Company further
covenants and agrees that the Company will at all times have authorized and
reserved, free from preemptive rights imposed by or through the Company, a
sufficient number of shares of Series E Preferred Stock and Common Stock to
provide for the exercise of the rights represented by this Warrant. The Company
further covenants and agrees that if any shares of capital stock to be reserved
for the purpose of the issuance of shares upon the exercise of this Warrant
require registration or qualification with or approval by the Securities and
Exchange Commission or any state regulatory agency under Federal or state law
(or by any analogous foreign regulatory body) before such shares may be validly
issued or delivered upon exercise, then the Company will in good faith and as
expeditiously as possible endeavor to secure such registration, qualification or
approval, as the case may be. Holders of Series E Preferred Stock and Common
Stock issuable upon exercise of this Warrant or conversion of any such shares,
as the case may be, shall be entitled to all the rights and privileges, and
bound by the obligations, of the Purchase Agreement, the Investor Rights
Agreement, and the Amended and Restated Voting Rights Agreement, all dated as of
the date hereof between the Company and the Investors (as defined therein) with
respect to such shares (the "Shareholder Agreements"). Upon exercise of the
Warrant, Warrant Holder at Company's request shall sign any counterpart
signature pages required in connection with becoming a party to such Shareholder
Agreements.

<PAGE>

     11. No Impairment. The Company will not voluntarily avoid or seek to avoid
the observance or performance of any of the terms of this Warrant, but will at
all times in good faith assist in the carrying out of all such terms and in the
taking of all such action as may be necessary or appropriate in order to protect
the rights of the Warrant Holder against impairment due to such event.

     12. Compliance with Securities Act.

     12.1 Unregistered Securities. The Warrant Holder acknowledges that this
Warrant and the Shares have not been registered under the Securities Act of
1933, as amended, and the rules and regulations thereunder, or any successor
legislation (the "Securities Act"), and agrees not to sell, pledge, distribute,
offer for sale, transfer or otherwise dispose of this Warrant or any Shares in
the absence of (i) an effective registration statement under the Securities Act
covering this Warrant or such Shares and registration or qualification of this
Warrant or such Shares under any applicable "blue sky" or state securities law
then in effect, or (ii) an opinion of counsel, satisfactory to the Company, that
such registration and qualification are not required. The Company may delay
issuance of the Shares until completion of any action or obtaining of any
consent, which the Company deems necessary under any applicable law (including
without limitation state securities or "blue sky" laws).

     12.2 Investment Representation. The Warrant Holder represents to the
Company that this Warrant is being acquired for the Warrant Holder's own account
and for the purpose of investment and not with a present view to, or for sale in
connection with, the distribution thereof, nor with any present intention of
distributing or selling the Warrant or Common Stock issuable upon exercise of
the Warrant. The Warrant Holder acknowledges that it has been afforded the
opportunity to meet with the management of the Company and to ask questions of,
and receive answers from, such management and the Company's counsel about the
business and affairs of the Company and concerning the terms and conditions of
the offering of this Warrant, and to obtain any additional information, to the
extent that the Company possessed such information or could acquire it without
unreasonable effort or expense, necessary to verify the accuracy of the
information otherwise obtained by or furnished to the Warrant Holder. The Holder
has received all information which the Warrant Holder considered necessary to
form a decision concerning the purchase of this Warrant, and no valid request to
the Company by the Warrant Holder hereof for information of any kind about the
Company has been refused or denied by the Company or remains unfulfilled as of
the date hereof. The Warrant Holder attests that it is considered to be a
sophisticated investor, is familiar with the risks inherent in speculative
investments such as in the Company, has such knowledge and experience in
financial business matters that he is capable of evaluating the merits and risk
of the investment in this Warrant and the Shares, and is able to bear the
economic risk of the investment. The Warrant Holder confirms that he is an
"accredited investor" as such term is defined in rule 501(a) of the Securities
Act.

     12.3 Investment Letter. Without limiting the generality of Section 12.1,
unless the offer and sale of any shares of Shares shall have been effectively
registered under the Securities Act, the Company shall be under no obligation to
issue the Shares unless and until the Warrant Holder shall have executed an
investment letter in form and substance satisfactory to the Company, including a
warranty at the time of such exercise that the Warrant Holder is acquiring such
shares for its own

<PAGE>

account, for investment and not with a view to, or for sale in connection with,
the distribution of any such shares.

     12.4 Legend. Certificates delivered to the Warrant Holder pursuant to
Section 2 shall bear the following legend or a legend in substantially similar
form (as well any such other legends as Company may reasonably require of its
shareholders generally):

     "THE SECURITIES REPRESENTED BY THIS CERTIFICATE HAVE NOT BEEN REGISTERED
     UNDER THE SECURITIES ACT OF 1933 OR ANY OTHER SECURITIES LAWS. THESE
     SECURITIES HAVE BEEN ACQUIRED FOR INVESTMENT AND NOT WITH A VIEW TO
     DISTRIBUTION OR RESALE. SUCH SECURITIES MAY NOT BE OFFERED FOR SALE, SOLD,
     DELIVERED AFTER SALE, TRANSFERRED, PLEDGED OR HYPOTHECATED IN THE ABSENCE
     OF AN EFFECTIVE REGISTRATION STATEMENT COVERING SUCH SECURITIES UNDER THE
     SECURITIES ACT OF 1933 AND ANY OTHER APPLICABLE SECURITIES LAWS, UNLESS THE
     HOLDER SHALL HAVE OBTAINED AN OPINION OF COUNSEL REASONABLY SATISFACTORY TO
     THE CORPORATION THAT SUCH REGISTRATION IS NOT REQUIRED."

     THE CORPORATION IS AUTHORIZED TO ISSUE MORE THAN ONE CLASS OR SERIES OF
     STOCK. THE CORPORATION WILL FURNISH WITHOUT CHARGE TO EACH STOCKHOLDER WHO
     SO REQUESTS THE POWERS, DESIGNATIONS, PREFERENCES AND RELATIVE,
     PARTICIPATING, OPTIONAL, OR OTHER SPECIAL RIGHTS OF EACH CLASS OF STOCK OR
     SERIES THEREOF AND THE QUALIFICATIONS, LIMITATIONS OR RESTRICTIONS OF SUCH
     PREFERENCES AND/OR RIGHTS.

     THE SHARES REPRESENTED HEREBY ARE ALSO SUBJECT TO RESTRICTIONS ON TRANSFER
     CONTAINED IN CERTAIN SUBSCRIPTION AND INVESTOR RIGHTS AGREEMENTS, AND MAY
     NOT BE SOLD, PLEDGED OR OTHERWISE TRANSFERRED WITHOUT COMPLIANCE WITH THE
     TERMS THEREOF. THE COMPANY WILL FURNISH A COPY OF THE FULL TEXT OF SUCH
     RESTRICTIONS TO THE HOLDER OF THIS CERTIFICATE UPON WRHTEN REQUEST AND
     WITHOUT CHARGE.

     THE SHARES EVIDENCED BY THIS CERTIFICATE ARE SUBJECT TO A CERTAIN AMENDED
     AND RESTATED VOTING AGREEMENT DATED AS OF _________, 20__ BY AND AMONG THE
     COMPANY AND THE STOCKHOLDERS OF THE COMPANY, A COPY OF WHICH AGREEMENT IS
     AVAILABLE FOR INSPECTION AT THE OFFICES OF THE COMPANY OR MAY BE OBTAINED
     FROM THE COMPANY UPON REQUEST AND WITHOUT CHARGE.

     13. Transferability. Without the prior written consent of the Company,
neither the Warrant nor the shares issuable upon exercise thereof (the "Warrant
Shares") shall be assigned, pledged or hypothecated in any way (whether by
operation of law or otherwise) or be subject to execution, attachment or similar
process. Any attempted transfer, assignment, pledge,

<PAGE>

hypothecation or other disposition of the Warrant, Warrant Shares, or of any
rights granted hereunder contrary to the provisions of this Section 13, or the
levy of any attachment or similar process upon the Warrant, Warrant Shares, or
such rights, shall be null and void. If, in connection with a registration
statement filed by the Company pursuant to the Securities Act of 1933, the
Company or its underwriter so requests, the Warrant Holder will agree not to
sell any Warrant Shares for a period not to exceed 180 days following the
effectiveness of such registration.

     14. Lost, Stolen, Mutilated or Destroyed Warrant. If this Warrant is lost,
stolen, mutilated or destroyed, the Company may, on such terms as to indemnity
or otherwise as it may reasonably in its discretion impose (which shall in the
case of a mutilated Warrant, include the surrender thereof), issue a new Warrant
of like denomination and tenor as the Warrant so lost, stolen, mutilated or
destroyed.

     15. Register of Warrants. The Company shall maintain, at the principal
office of the Company (or such other office as it may designate by notice to the
Warrant Holder), a register for the Warrants in which the Company shall record
the name and address of the person in whose name a Warrant has been issued, as
well as the name and address of each transferee and each prior owner of such
Warrant.

     16. Miscellaneous.

     16.1 Waivers and Amendments. This Warrant or any provisions hereof may be
changed, waived, discharged or terminated only by a statement in writing signed
by the Company and by Warrant Holders who hold or have the right to acquire at
least two-thirds of the Shares at such time issued or issuable upon exercise of
the Warrants, provided that no change, addition, omission or waiver shall be
made without the written consent of the Warrant Holder(s) which affects (i) the
number of Shares issuable on exercise of this Warrant, (ii) the Exercise Price
or (iii) any other provision other than in a manner in which all the Warrants
are affected.

     16.2 Governing Law. This Agreement shall be governed by and construed and
enforced in accordance with the laws of the State of Delaware (US) without
giving effect to the conflicts of laws principles thereof.

     16.3 Notices. All notices or other communications required or permitted
hereunder shall be in writing and shall be hand delivered, sent by facsimile or
other electronic medium, or mailed, postage prepaid, or sent by reputable
overnight courier, delivery charges prepaid, addressed as follows or to such
other address as may be furnished in writing to the other parties hereto:

     If to the Warrant Holder: Three Crowns Capital (Bermuda) Ltd.
                               Suite 1139
                               48 Par-La-Ville Road
                               Hamilton HM11
                               Bermuda
                               441-293 7107 (Fax)
                               Attention: Peter Svennilson

     With a copy to:           Conyers Dill & Pearman

<PAGE>

                               Clarendon House
                               2 Church Street
                               Hamilton HM 11
                               Bermuda
                               441-292-4720 (Fax)
                               Attention: Peter A. S. Pearman

     And:                      Nixon Peabody LLP
                               101 Federal Street
                               Boston, MA 02110
                               617-345-1300 (Fax)
                               Attention: Carter S. Bacon, Esq.

     If to the Company:        PTC Therapeutics, Inc.
                               Attention: Legal Department
                               100 Corporate Court
                               Middlesex Business Center
                               South Plainfield, NJ 07080

                               with an email copy to: legal@ptcbio.com

     With a copy to:           Wilmer Cutler Pickering Hale and Dorr LLP
                               60 State Street
                               Boston, Massachusetts 02109
                               Attn: David E. Redlick, Esq.

     All such notices and communications shall be deemed to have been duly given
(i) five (5) business days after being deposited in the mail, postage prepaid if
mailed, (ii) one (1) business day after being sent by overnight courier, (iii)
when receipt acknowledged if telecopied and (iv) upon receipt if delivered by
hand.

     16.4 Headings. The headings in this Warrant are for convenience of
reference only and shall not limit or otherwise affect the terms hereof.

     16.5 Remedies. The Company stipulates that the remedies at law of the
holder of this Warrant in the event of any default or threatened default by the
Company in the performance of or compliance with any of the terms of this
Warrant are not and will not be adequate, and that such terms may be
specifically enforced by a decree for the specific performance of any agreement
contained herein or by an injunction against a violation of any of the terms
hereof or otherwise.

     16.6 Currency. All currency references herein are to United States Dollars.

     16.7 Closing of Books. The Company will at no time close its transfer books
against the transfer of any Warrant or of any Shares issued or issuable upon the
exercise of the Warrant in a manner which interferes with the timely exercise of
this Warrant.

     16.8 No Rights or Liabilities as a Stockholder. This Warrant shall not
entitle the Warrant Holder to any voting rights or other rights as a stockholder
of the Company prior to the

<PAGE>

exercise or conversion of the Warrant, provided that nothing herein shall be
construed to limit or impair other rights that the Warrant Holder may have under
this Warrant or otherwise. No provision of this Warrant, in the absence of
affirmative action by the Warrant Holder to purchase the Shares, and no mere
enumeration herein of the rights or privileges of the Warrant Holder, shall give
rise to any liability of such Warrant Holder for the Exercise Price or as a
stockholder of the Company, whether such liability is asserted by the Company or
by creditors of the Company.

<PAGE>

     IN WITNESS WHEREOF, the undersigned has caused this Warrant to be executed
as an instrument under seal.

                                   PTC Therapeutics, Inc.


                                   By: /s/ MARK E. BOULDING
                                       ------------------------------------
                                   Name: Mark E. Boulding
                                         ----------------------------------
                                   Title: S.V.P., Business Development and Legal
                                          ---------------------------------


AGREED AND ACKNOWLEDGED:

THREE CROWNS CAPITAL (BERMUDA) LTD.



<PAGE>

                                    EXHIBIT A

                    NOTICE OF EXERCISE OR NET ISSUE EXERCISE

                                                         Date: ________ __, 20__

YY

Gentlemen:

The undersigned hereby elects to exercise or Net Issue Exercise the enclosed
Warrant issued by YY (the "Company") and dated as of ____ __, 2003.

     The undersigned elects to:

     [ ]  Exercise the Warrant and to purchase thereunder _____ shares of the
          Series __ Preferred Stock of the Company (the "Shares") at an exercise
          price of _____ per Share for an aggregate purchase price of _________
          (the "Purchase Price"). Pursuant to the terms of the Warrant, the
          undersigned has delivered the Purchase Price herewith in full.

     [ ]  Net Issue Exercise ____% of the value of the Warrant at the current
          Exercise Price (as defined in the Warrant) of ____ per Share.

                                        Very truly yours,


                                        ----------------------------------------