Exhibit 3.1  AMENDED
AND RESTATED CERTIFICATE
OF INCORPORATION OF ARYX
THERAPEUTICS, INC.  ARYX THERAPEUTICS, INC.,
a corporation organized and existing under the laws of the state of Delaware
(the Corporation) hereby certifies that:  ONE:The
original name of this corporation is ARYx Therapeutics, Inc. and the date of
filing of the original Certificate of Incorporation of this corporation with
the Secretary of State of the State of Delaware was August 6, 2007.  TWO:This
Amended and Restated Certificate of Incorporation has been duly approved by the
Board of Directors of the Corporation (the Board).  THREE:This Amended and Restated Certificate of
Incorporation was approved by the holders of the requisite number of shares of
the Corporation in accordance with Section 228 of the General Corporation Law
of the State of Delaware. This Amended and Restated Certificate of
Incorporation has been duly adopted in accordance with the provisions of
Sections 242 and 245 of the General Corporation Law of the State of Delaware by
the stockholders of said corporation.  FOUR:The
Amended and Restated Certificate of Incorporation so adopted reads in full as
set forth in EXHIBIT Aattached hereto and is
incorporated herein by reference in its entirety.  IN WITNESS WHEREOF,
the Corporation has caused this Amended and Restated Certificate of
Incorporation to be signed by its Chairman of the Board and Chief Executive
Officer this 13th day of November, 2007.   ARYX
  THERAPEUTICS, INC.By
  /s/
  Paul GoddardPAUL GODDARDChairman of
  the Board and Chief
  Executive Officer  1


Exhibit A  AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
OF
ARYX THERAPEUTICS, INC.  I.  The name of this corporation is ARYX THERAPEUTICS, INC.(the Corporation).  II.  The address, including
street, number, city, and county, of the registered office of the Corporation
in the State of Delaware is 615 South Dupont Highway, City of Dover, 19901,
County of Kent; and the name of the registered agent of the Corporation in the
State of Delaware at such address is National Corporate Research, Ltd.  III.  The purpose of the Corporation is to engage
in any lawful act or activity for which a corporation may be organized under
the Delaware General Corporation Law (DGCL).  IV.  A.The Corporation is authorized to issue two
classes of stock to be designated, respectively, Common Stock and Preferred Stock.  The total number of shares which the
Corporation is authorized to issue is one hundred sixty million (160,000,000)
shares. One hundred fifty million (150,000,000) shares shall be Common Stock,
each having a par value of one-tenth of one cent ($0.001). Ten million
(10,000,000) shares shall be Preferred Stock, each having a par value of
one-tenth of one cent ($0.001).  B.The Preferred Stock may be issued from time
to time in one or more series. The Board of Directors is hereby expressly
authorized to provide for the issue of all of any of the remaining shares of the Preferred
Stock in one or more series, and to fix the number of shares and to determine
or alter for each such series, such voting powers, full or limited, or no
voting powers, and such designation, preferences, and relative, participating,
optional, or other rights and such qualifications, limitations, or restrictions
thereof, as shall be stated and expressed in the resolution or resolutions
adopted by the Board of Directors providing for the issuance of such shares and
as may be permitted by the DGCL. The Board of Directors is also expressly
authorized to increase or decrease the number of shares of any series
subsequent to the issuance of shares of that series, but not below the number
of shares of such series then outstanding. In case the number of shares of any
series shall be decreased in accordance with the foregoing sentence, the shares
constituting such decrease shall resume the status that they had prior to the
adoption of the resolution originally fixing the number of shares of such
series. The number of authorized shares of Preferred Stock may be increased or
decreased (but not below the number of shares thereof then outstanding) by the
affirmative vote of the holders of a majority of the Common Stock, without a
vote of the holders of the Preferred Stock, or of any series thereof,  2


unless
a vote of any such holders is required pursuant to the terms of any certificate
of designation filed with respect to any series of Preferred Stock.  C.Each outstanding share of Common Stock shall
entitle the holder thereof to one vote on each matter properly submitted to the
stockholders of the Corporation for their vote; provided,
however, that, except as otherwise required by law, holders of
Common Stock shall not be entitled to vote on any amendment to this Certificate
of Incorporation (including any certificate of designation filed with respect
to any series of Preferred Stock) that relates solely to the terms of one or
more outstanding series of Preferred Stock if the holders of such affected
series are entitled, either separately or together as a class with the holders
of one or more other such series, to vote thereon by law or pursuant to this
Certificate of Incorporation (including any certificate of designation filed
with respect to any series of Preferred Stock).  V.  For the management of the business and for
the conduct of the affairs of the Corporation, and in further definition,
limitation and regulation of the powers of the Corporation, of its directors
and of its stockholders or any class thereof, as the case may be, it is further
provided that:  A.  1.MANAGEMENT OF BUSINESS.The management of the business and the
conduct of the affairs of the Corporation shall be vested in its Board of
Directors. The number of directors which shall constitute the Board of
Directors shall be fixed exclusively by resolutions adopted by a majority of
the authorized number of directors constituting the Board of Directors.  2.BOARD OF DIRECTORS.  a.Subject
to the rights of the holders of any series of Preferred Stock to elect
additional directors under specified circumstances, immediately following the
closing of the firm underwritten initial public offering pursuant to an
effective registration statement under the Securities Act of 1933, as amended,
covering the offer and sale of Common Stock to the public (the Initial
Public Offering), the directors shall be divided into three classes
designated as Class I, Class II and Class III, respectively. At the first
annual meeting of stockholders following the closing of the Initial Public
Offering, the term of office of the Class I directors shall expire and Class I
directors shall be elected for a full term of three years. At the second annual
meeting of stockholders following the Initial Public Offering, the term of
office of the Class II directors shall expire and Class II directors shall be
elected for a full term of three years. At the third annual meeting of
stockholders following the Initial Public Offering, the term of office of the
Class III directors shall expire and Class III directors shall be elected for a
full term of three years. At each succeeding annual meeting of stockholders,
directors shall be elected for a full term of three years to succeed the
directors of the class whose terms expire at such annual meeting.  b.During
such time or times that the corporation is subject to Section 2115(b) of the
California General Corporation Law (CGCL), Section A. 2. a. of this
Article V  3


shall not apply and all
directors shall be elected at each annual meeting of stockholders to hold
office until the next annual meeting.  c.No
stockholder entitled to vote at an election for directors may cumulate votes to
which such stockholder is entitled, unless, at the time of such election, the
corporation is subject to Section 2115(b) of the CGCL. During such time or
times that the corporation is subject to Section 2115(b) of the CGCL, every
stockholder entitled to vote at an election for directors may cumulate such
stockholders votes and give one candidate a number of votes equal to the
number of directors to be elected multiplied by the number of votes to which
such stockholders shares are otherwise entitled, or distribute the stockholders
votes on the same principle among as many candidates as such stockholder thinks
fit. No stockholder, however, shall be entitled to so cumulate such stockholders
votes unless (i) the names of such candidate or candidates have been placed in
nomination prior to the voting and (ii) the stockholder has given notice at the
meeting, prior to the voting, of such stockholders intention to cumulate such
stockholders votes. If any stockholder has given proper notice to cumulate
votes, all stockholders may cumulate their votes for any candidates who have
been properly placed in nomination. Under cumulative voting, the candidates
receiving the highest number of votes, up to the number of directors to be
elected, are elected.  d.Notwithstanding
the foregoing provisions of this section, each director shall serve until his
successor is duly elected and qualified or until his death, resignation or
removal. No decrease in the number of directors constituting the Board of
Directors shall shorten the term of any incumbent director.  3.REMOVAL.  a.During
such time or times that the corporation is subject to Section 2115(b) of the
CGCL, the Board of Directors or any individual director may be removed from
office at any time without cause by the affirmative vote of the holders of at
least a majority of the outstanding shares entitled to vote on such removal; provided, however, that unless the entire Board is removed,
no individual director may be removed when the votes cast against such directors
removal, or not consenting in writing to such removal, would be sufficient to
elect that director if voted cumulatively at an election which the same total
number of votes were cast (or, if such action is taken by written consent, all
shares entitled to vote were voted) and the entire number of directors authorized
at the time of such directors most recent election were then being elected.  b.At
any time or times that the corporation is not subject to Section 2115(b) of the
CGCL and subject to any limitations imposed by law, Section A. 3. a. above
shall no longer apply and removal shall be as provided in Section 141(k) of the
DGCL.  4.VACANCIES.  a.Subject to the rights of the holders of any
series of Preferred Stock, any vacancies on the Board of Directors resulting
from death, resignation, disqualification, removal or other causes and any
newly created directorships resulting from any increase in the  4


number
of directors, shall, unless the Board of Directors determines by resolution
that any such vacancies or newly created directorships shall be filled by the
stockholders, except as otherwise provided by law, be filled only by the
affirmative vote of a majority of the directors then in office, even though
less than a quorum of the Board of Directors, and not by the stockholders. Any
director elected in accordance with the preceding sentence shall hold office
for the remainder of the full term of the director for which the vacancy was
created or occurred and until such directors successor shall have been elected
and qualified.  b.If at the time of filling any vacancy or any
newly created directorship, the directors then in office shall constitute less
than a majority of the whole board (as constituted immediately prior to any
such increase), the Delaware Court of Chancery may, upon application of any
stockholder or stockholders holding at least ten percent (10%) of the total
number of the shares at the time outstanding having the right to vote for such
directors, summarily order an election to be held to fill any such vacancies or
newly created directorships, or to replace the directors chosen by the
directors then in office as aforesaid, which election shall be governed by
Section 211 of the DGCL.  c.At any time or times that the corporation is
subject to Section 2115(b) of the CGCL, if, after the filling of any vacancy by
the directors then in office who have been elected by stockholders shall
constitute less than a majority of the directors then in office, then:  (i)Any holder or holders of an aggregate of five
percent (5%) or more of the total number of shares at the time outstanding
having the right to vote for those directors may call a special meeting of
stockholders; or  (ii)The Superior Court of the proper county
shall, upon application of such stockholder or stockholders, summarily order a
special meeting of stockholders, to be held to elect the entire board, all in
accordance with Section 305(c) of the CGCL. The term of office of any director
shall terminate upon that election of a successor.  B.  1.BYLAW AMENDMENTS.The Board of Directors is expressly empowered
to adopt, amend or repeal the Bylaws of the Corporation. Any adoption,
amendment or repeal of the Bylaws of the corporation by the Board of Directors
shall require the approval of a majority of the authorized number of directors.
The stockholders shall also have power to adopt, amend or repeal the Bylaws of
the Corporation; provided, however, that, in
addition to any vote of the holders of any class or series of stock of the
Corporation required by law or by this Amended and Restated Certificate of
Incorporation, the affirmative vote of the holders of at least sixty-six and two-thirds percent (66 2/3%)
of the voting power of all of the then-outstanding shares of the capital stock
of the Corporation entitled to vote generally in the election of directors,
voting together as a single class, shall be required to adopt, amend or repeal
any provision of the Bylaws of the Corporation.  5


2.WRITTEN BALLOT.The directors of the Corporation need not be
elected by written ballot unless the Bylaws so provide.  3.NO WRITTEN CONSENT.No action shall be taken by the stockholders
of the Corporation except at an annual or special meeting of stockholders called
in accordance with the Bylaws or by written consent or electronic transmission
of stockholders in accordance with the Bylaws prior to the closing of the
Initial Public Offering, and following the closing of the Initial Public
Offering, no action shall be taken by the stockholders by written consent or
electronic transmission.  4.ADVANCE NOTICE PROVISIONS.Advance notice of stockholder nominations for
the election of directors and of business to be brought by stockholders before
any meeting of the stockholders of the Corporation shall be given in the manner
provided in the Bylaws of the Corporation.  VI.  A.The liability of the directors and executive
officers (for the purposes of this Article VI, executive officers shall have
the meaning defined in Rule 3b-7 promulgated under the Securities Exchange Act
of 1934, as amended) of the Corporation
for monetary damages shall be eliminated to the fullest extent under applicable
law. If the DGCL is amended to authorize corporate action further eliminating
or limiting the personal liability of directors and executive officers, then
the liability of a director or executive officer of the Corporation shall be
eliminated to the fullest extent permitted by the DGCL, as so amended.  B.The Corporation is authorized to provide
indemnification of agents (as defined in Section 317 of the CGCL) for breach of
duty to the Corporation and its stockholders through bylaw provisions or
through agreements with the agents, or through stockholder resolutions, or
otherwise, in excess of the indemnification otherwise permitted by Section 317
of the CGCL, subject, at any time or times the Corporation is subject to
Section 2115(b), to the limits on such excess indemnification set forth in
Section 204 of the CGCL.  C.Any repeal or modification of this
Article VI shall be prospective and shall not affect the rights under this
Article VI in effect at the time of the alleged occurrence of any act or
omission to act giving rise to liability or indemnification.  VII.  A.The Corporation reserves the right to amend,
alter, change or repeal any provision contained in this Amended and Restated
Certificate of Incorporation, in the manner now or hereafter prescribed by
statute, except as provided in paragraph B. of this Article VII, and all
rights conferred upon the stockholders herein are granted subject to this
reservation.  B.Notwithstanding any other provisions of this
Amended and Restated Certificate of Incorporation or any provision of law which
might otherwise permit a lesser vote or no vote, but in addition to any
affirmative vote of the holders of any particular class or series of the
Corporation required by law or by this Amended and Restated Certificate of
Incorporation or any certificate of designation filed with respect to a series of
Preferred Stock, the affirmative vote of  6


the
holders of at least sixty-six and two-thirds percent (66-2/3%) of the voting
power of all of the then-outstanding shares of capital stock of the Corporation
entitled to vote generally in the election of directors, voting together as a
single class, shall be required to alter, amend or repeal Articles V, VI, and
VII.  ***  7