Document:

Amendment Number Two to Savings Plan for Subsidiaries of SunCoke Energy, Inc.

 Exhibit 4.6 
 AMENDMENT NUMBER TWO 
 TO THE 

SAVINGS PLAN FOR SUBSIDIARIES OF SUNCOKE ENERGY, INC. 
 This Amendment Number Two (“Amendment”) to the Savings Plan for Subsidiaries of SunCoke Energy, Inc. (the “Plan”), is adopted by the Committee designated by SunCoke Energy, Inc. (the
“Company”), and is effective as of January 1, 2012, unless otherwise set forth below. 
 WHEREAS, the
Company maintains the Plan for the benefit of certain eligible employees; and 
 WHEREAS, pursuant to Section 12.01
of the Plan, the Company has the right to amend the Plan; and 
 WHEREAS, pursuant to Sections 11.03(c)(10) and 12.01(b)
of the Plan, the Committee has the power to make amendments that do not materially increase the costs associated with the Plan; and 
 WHEREAS, the Committee desires to amend the Plan (i) so that the Schedule applicable to Gateway Energy and Coke Company, LLC is consistent with the terms of the applicable collective
bargaining agreement, which the Company previously approved; (ii) to provide for the transfer of assets between the Plan and the SunCoke Profit Sharing and Retirement Plan, in certain circumstances; and (iii) to clarify the vesting schedule
applicable to Dominion Coal Corporation. 
 NOW, THEREFORE, BE IT RESOLVED, that the Plan is hereby amended as follows:

 FIRST CHANGE 
 Effective January 1, 2011, Article 4 is amended by adding a Section 4.08 that shall read as follows: 
 “4.08 Transfer of Assets. 
  

	 	(a)	With respect to any Participant who was previously a participant in the SunCoke Profit Sharing and Retirement Plan (“Profit Sharing Plan”) and subsequently
becomes a Participant in this Plan, the Plan Administrator may direct the Trustee to accept a transfer of the Participant’s assets (including any outstanding loan(s)) from the Profit Sharing Plan. 

 

	 	(b)	With respect to any Participant who ceases to actively participate in this Plan and subsequently becomes a participant in the Profit Sharing Plan, the Plan
Administrator may direct the Trustee to transfer the Participant’s Plan assets (including any outstanding loan(s)) to the Profit Sharing Plan, provided the Profit Sharing Plan’s trustee will accept the transfer.”

 SECOND CHANGE 

Appendix A is amended to read as follows: 
 “PARTICIPATING EMPLOYERS 
  

			
	 Participating Employer
	  	 Effective Date of Affiliation

	Dominion Coal Corporation	  	September 1, 2005
	Haverhill North Coke Company	  	January 1, 2005
	Gateway Energy and Coke Company, LLC (a/k/a Granite City)	  	February 1, 2010”

 THIRD CHANGE 
 Effective January 1, 2011, the provisions under Section E of Schedule A are replaced with the following: 
  

	 	“(a)	Any Participant who terminates Employment for any reason other than Retirement shall be vested in his Profit Sharing Contribution Account and Employer Matching
Contribution Account pursuant to the following vesting schedule: 

  

					
	 Years of Vesting Service
	  	Vested Percentage	 
	 Less than 2 Years
	  	 	0	% 
	 2 Years
	  	 	20	% 
	 3 Years
	  	 	40	% 
	 4 Years
	  	 	80	% 
	 5 Years or More
	  	 	100	% 

 Effective January 1, 2011, the vesting schedule in this subparagraph (a) shall apply only to
those Participants that were not Employees of the Participating Employer as of December 31, 2010 (and who were not rehired by the Participating Employer after such date). 

 

	 	(b)	Effective January 1, 2011, any Participant (i) who was an Employee of the Participating Employer on January 1, 2011 (or who was not an Employee on such
date but was/is later rehired by the Participating Employer) and (ii) who terminates Employment for any reason other than Retirement on or after January 1, 2011 shall be vested in his Profit Sharing Contribution Account and Employer
Matching Contribution Account pursuant to the following vesting schedule: 

  
 2 

					
	 Years of Vesting Service
	  	Vested Percentage	 
	 Less than 3 Years
	  	 	0	% 
	 3 Years or More
	  	 	100	% 

 Notwithstanding anything herein to the contrary, the vesting schedule in this subparagraph (b) shall
not have the effect of reducing any Participant’s vested benefit as of December 31, 2010. 
  

	 	(c)	Notwithstanding the forgoing schedules in subparagraphs (a) and (b), any Participant who terminates Employment by reason of death shall immediately become 100%
vested in his or her Profit Sharing Contribution Account and Employer Matching Contribution Account. 

  

	 	(d)	Notwithstanding the foregoing schedules in subparagraphs (a) and (b), pursuant to Section 13.11(d) of the Main Plan Document, Safe Harbor Contributions shall
be 100% vested upon contribution to the Plan.” 

 FOURTH CHANGE 

The definition of “Compensation” in Schedule C shall be amended to include the following language at the end of
subparagraph (a): 
 “Notwithstanding the foregoing, Compensation shall not include all of the following items (even if
includible in gross income): reimbursements or other expense allowances, fringe benefits (cash and noncash), moving expenses, deferred compensation, and welfare benefits.” 
 FIFTH CHANGE 
 The definition of “Eligible Employee” in Schedule
C shall be amended to read as follows: 
 “Eligible Employee. Only Employees of the Participating Employer who are
covered by a collective bargaining agreement, which provides for such Employee’s participation in the Plan, shall be Eligible Employees.” 
 SIXTH CHANGE 
 The definition of “Entry Date” in Schedule C shall
be amended to read as follows: 
 “Entry Date. As soon as administratively feasible upon the Participant meeting the
service requirements set forth in this Schedule.” 

  
 3 

 SEVENTH CHANGE 

The definition of “Participating Employer” in Schedule C is amended to read as follows: 

“Participating Employer. For purposes of this Schedule C, the Participating Employer is Granite City.” 

EIGHTH CHANGE 
 The provisions under Section B of Schedule C are replaced with the following: 

“An Employee of the Participating Employer who is not eligible to participate in the Plan on January 1, 2012 shall become a
Participant in the Plan on the first Entry Date following (i) the date the Eligible Employee has completed one (1) Hour of Service or (ii) the date the Employee becomes an Eligible Employee, whichever is later.” 

NINTH CHANGE 
 The provisions under Section C of Schedule C are replaced with the following: 

“At the end of each payroll period, the Employer will make an Employer Matching Contribution to the Plan. The Employer Matching
Contribution shall be equal to 100% of the Participant’s Pre~Tax Contributions and Catch-Up Contributions for the payroll period, with such Employer Matching Contribution not to exceed 5% of the Participant’s Compensation for such payroll
period.” 
 TENTH CHANGE 
 The provisions under Section E of Schedule C are replaced with the following: 
  

	 	“(a)	Any Participant who terminates Employment for any reason other than Retirement shall be vested in his Profit Sharing Contribution Account and Employer Matching
Contribution Account pursuant to the following vesting schedule: 

  

					
	 Years of Vesting Service
	  	Vested Percentage	 
	 Less than 2 Years
	  	 	0	% 
	 2 Years
	  	 	20	% 
	 3 Years
	  	 	40	% 
	 4 Years
	  	 	80	% 
	 5 Years or More
	  	 	100	% 

 Effective January 1, 2012, the vesting schedule in this subparagraph (a) shall apply only to
those Participants that were not Employees of the Participating Employer as of December 31, 2011 (and who were not rehired by the Participating Employer after such date). 

  
 4 

	 	(b)	Effective January 1, 2012, any Participant (i) who is an Employee of the Participating Employer on January 1, 2012 (or who is not an Employee on such
date but is later rehired by the Participating Employer) and (ii) who terminates Employment for any reason other than Retirement on or after January 1, 2012 shall be vested in his Profit Sharing Contribution Account and Employer Matching
Contribution Account pursuant to the following vesting schedule: 

  

					
	 Years of Vesting Service
	  	Vested Percentage	 
	 Less than 3 Years
	  	 	0	% 
	 3 Years or More
	  	 	100	% 

 Notwithstanding anything herein to the contrary, the vesting schedule in this subparagraph (b) shall
not have the effect of reducing any Participant’s vested benefit as of December 31,2011. 
  

	 	(c)	Notwithstanding the forgoing schedules in subparagraphs (a) and (b), any Participant who terminates Employment by reason of death shall immediately become 100%
vested in his or her Profit Sharing Contribution Account and Employer Matching Contribution Account. 

  

	 	(d)	Notwithstanding the foregoing schedules in subparagraphs (a) and (b), pursuant to Section 13.11(d) of the Main Plan Document, Safe Harbor Contributions shall
be 100% vested upon contribution to the Plan.” 

 ELEVENTH CHANGE 

The provisions under Section G of Schedule C are replaced with the following: 

“In accordance with Article 10 of the Main Plan Document, a Participant employed by the Participating Employer may take a loan from
the Plan.” 
 TWELFTH CHANGE 
 Schedule C is amended to add the following Section H: 
 “Section H: Safe
Harbor Provision 
 Section 13.11 of the Main Plan Document shall apply to the Participating Employer and its Eligible
Employees.” 

  
 5 

 THIRTEENTH CHANGE 

The provisions under Section G of Schedule A are replaced with the following: 

“In accordance with Article 10 of the Main Plan Document, a Participant employed by the Participating Employer may take a loan from
the Plan.” 
 IN WITNESS WHEREOF, the Committee has caused this Amendment to the Plan to be executed on the
date shown below, but effective as of the respective effective date(s) set forth above. 
  

	
	SUNCOKE ENERGY, INC.
	
	By:       /s/Gary Yeaw                  
                                  
	Title:    VICE PRESIDENT-HUMAN RESOURCES
	Date:    11/20/11

  
 6First Amendment to Stock Purchase Agreement

 Exhibit 10.10 
 CONFIDENTIAL TREATMENT REQUESTED 
 Redacted portions are indicated by
[****] 
 Redacted portions filed separately 
 with Confidential Treatment Application. 
 FIRST AMENDMENT TO

 STOCK PURCHASE AGREEMENT 
 THIS FIRST AMENDMENT TO STOCK PURCHASE AGREEMENT (this “Amendment”) is effective as of April 13, 2012 and amends that certain Stock Purchase Agreement, dated as of February 4,
2010 (the “Agreement”), by and among BioMarin Pharmaceutical Inc., a Delaware corporation (the “Buyer”), LEAD Therapeutics, Inc., a Delaware corporation (the “Company”), the parties listed on Schedule A to
the Agreement (each a “Seller” and collectively the “Sellers”) and Arthur Pappas, acting in his capacity as Equityholder Representative in connection with the transactions contemplated by the Agreement (the “Equityholder
Representative”). (Hereafter, Buyer, the Company, each Seller and the Equityholder Representative shall sometimes be referred to as the “Parties”). 
 RECITALS 
 A. WHEREAS, pursuant to the Agreement, the Sellers sold,
assigned, transferred and delivered to the Purchaser, and the Purchaser purchased and acquired from the Sellers, all right, title and interest in and to all of the issued and outstanding shares of capital stock of the Company; 

B. WHEREAS, pursuant to Section 11.4 of the Agreement, the Agreement may not be amended, modified or supplemented except by written
agreement between the Parties; and 
 C. WHEREAS, the Parties desire to modify the Agreement as set forth in this Amendment.

 NOW, THEREFORE, in consideration of the foregoing, the parties hereto hereby agree as follows: 

1. Each of the defined terms set forth below and in Section 1.1 of the Agreement shall be deleted in their entirety and replace with
the following new defined terms: 
 “Milestone Payment Amounts” means the First PARP Subsequent Payment Amount,
if any, the Second PARP Subsequent Payment Amount, if any, the Third PARP Subsequent Payment Amount, if any, the Fourth PARP Subsequent Payment Amount, if any, each Non-PARP Phase 2 Payment Amount, if any, each Non-PARP Phase 3 Payment Amount, if
any, each Non-PARP Sublicensing Payment Amount, if any, the Dose Escalation Study Subsequent Payment Amount, if any, and the Non-PARP Sublicensing Clinical Payment Amount, if any. 

  
 [***]=Certain confidential
information contained in this document, marked by brackets, has been omitted and filed separately with the Securities and Exchange Commission pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as amended. 

 “Non-PARP Phase 2 Milestone” means [****] 

“Non-PARP Phase 2 Payment Amount” means [****] 

“Non-PARP Phase 3 Milestone” means [****] 

“Non-PARP Phase 3 Payment Amount” means [****] 

“Non-PARP Sublicensing Payment Amount” means [****] 

“Non-PARP Sublicensing Payment Date” means the fifteenth (15th) Business Day following the Buyer’s receipt of the Future
Payment Allocation Schedule relating to the distribution to Equityholders of any Non-PARP Sublicensing Payment Amount in accordance with Section 2.1(l). 
 2. The following new defined terms shall be added to Section 1.1 of the Agreement: 
 “Non-PARP Sublicensing Clinical Milestone” means [****]  

“Non-PARP Sublicensing Clinical Payment Amount” means [****]  

“Non-PARP Sublicensing Clinical Payment Date” means the fifteenth (15th) Business Day following the Buyer’s receipt of the Future
Payment Allocation Schedule relating to the distribution to Equityholders of any Non-PARP Sublicensing Clinical Payment Amount in accordance with Section 2.1(n). 
 3. Subsection (m) of Section 2.1 of the Agreement shall be deleted and replaced with the subsection (m) set forth below and the following new subsection (n) shall be added at the end
of Section 2.1 of the Agreement: 
 (m) the Dose Escalation Study Subsequent Payment Amount, if any, payable on the Dose
Escalation Study Subsequent Payment Date (with the portion of the Dose Escalation Study Subsequent Payment Amount that is payable to each Equityholder determined as set forth on a Future Payment Allocation Schedule related to the Dose Escalation
Study Subsequent Payment Amount); plus 
 (n) the Non-PARP Sublicensing Clinical Payment Amount, if any, payable on the Non-PARP
Sublicensing Clinical Payment Date (with the portion of each Non-PARP Sublicensing Clinical Payment Amount that is payable to each Equityholder determined as set forth on a Future Payment Allocation Schedule related to such Non-PARP Sublicensing
Clinical Payment Amount). 
 4. Capitalized terms used in this Amendment but not otherwise defined herein shall have the
meanings set forth in the Agreement. 
 5. Except as expressly set forth in this Amendment, all other terms of the Agreement
shall remain in full force and effect and once this Amendment is executed by the parties hereto, all references in the Agreement to “the Agreement” or “this Agreement,” as applicable, shall refer to the Agreement, as modified by
this Amendment. 

  
 [***]=Certain confidential
information contained in this document, marked by brackets, has been omitted and filed separately with the Securities and Exchange Commission pursuant to Rule 24b-2 of the Securities Exchange Act of 1934, as amended. 

 8. This Amendment shall be construed, interpreted and the rights of the Parties determined
in accordance with the laws of the State of Delaware, as applied to agreements among Delaware residents entered into and wholly to be performed within the State of Delaware (without reference to any choice of law rules that would require the
application of the laws of any other jurisdiction). 
 9. This Amendment will apply to, be binding in all respects upon and
inure to the benefit of the successors and permitted assigns of the parties. 
 10. This Amendment may be executed in several
counterparts, each of which shall be deemed an original and all of which shall constitute one and the same instrument, and shall become effective when counterparts have been signed by each of the parties and delivered to the other parties; it being
understood that all parties need not sign the same counterparts. The exchange of copies of this Amendment and of signature pages by facsimile transmission (whether directly from one facsimile device to another by means of a dial-up connection or
whether mediated by the worldwide web), by electronic mail in “portable document format” (“.pdf”) form, or by any other electronic means intended to preserve the original graphic and pictorial appearance of a document, or by
combination of such means, shall constitute effective execution and delivery of this Amendment as to the parties and may be used in lieu of the original Amendment for all purposes. Signatures of the parties transmitted by facsimile or other
electronic means shall be deemed to be their original signatures for all purposes. 
 [Signature Page Follows] 

 IN WITNESS WHEREOF, the parties hereto have executed and delivered this Amendment as of the
date first above written. 
  

			
	BIOMARIN PHARMACEUTICAL INC.
		
	By:	 	/S/ G. Eric Davis
		 	Name: G. Eric Davis
		 	Title: S.V.P., General Counsel

  

			
	LEAD THERAPEUTICS, INC.
		
	By:	 	/S/ G. Eric Davis
		 	Name: G. Eric Davis
		 	Title: Vice President

  

			
	EQUITYHOLDER REPRESENTATIVE:
		
	By:	 	/S/_Arthur Pappas
		 	Arthur Pappas, as Equityholder Representative

  
 SIGNATURE
PAGE TO FIRST AMENDMENT TO STOCK PURCHASE AGREEMENT 

 
			
	SELLERS
		
		 	PROQUEST INVESTMENTS IV, L.P.
	 By:
	 	ProQuest Associates IV LLC, its General Partner
		
	 By:
	 	/S/ Pasquale DeAngelis
	 Name:
	 	Pasquale DeAngelis
	 Title:
	 	Managing Member

  

			
		 	PROQUEST MANAGEMENT LLC
		
	 By:
	 	/S/ Pasquale DeAngelis
	 Name:
	 	Pasquale DeAngelis
	 Title:
	 	Chief Financial Officer and Administrative Partner

  
 SIGNATURE
PAGE TO FIRST AMENDMENT TO STOCK PURCHASE AGREEMENT 

 
			
	SELLERS
		
		 	A. M. PAPPAS LIFE SCIENCE VENTURES III, LP
	 By:
	 	AMP&A Management III, LLC, its General Partner
		
	 By:
	 	/S/ Ford S. Worthy
	 Name:
	 	Ford S. Worthy
	 Title:
	 	Partner

  

			
		 	PV III CEO FUND, LP
	 By:
	 	AMP&A Management III, LLC, its General Partner
		
	 By:
	 	/S/ Ford S. Worthy
	 Name:
	 	Ford S. Worthy
	 Title:
	 	Partner

  
 SIGNATURE
PAGE TO FIRST AMENDMENT TO STOCK PURCHASE AGREEMENT 

 
			
	SELLERS
		
		 	MUSTANG VENTURES I, L.P.
	 By:
	 	
		
	 By:
	 	/S/ Robert C. McCormack, Jr.
	 Name:
	 	Robert C. McCormack, Jr.
	 Title:
	 	Managing Director

 
	
	SELLERS
	
	CHINA GATEWAY LIFE SCIENCE (HOLDINGS) LTD. (HK)
	
	Print Name:
	
	    Michael Hui
	
	Title:
	
	    CEO
	
	Signature:
	
	    /S/ Michael Hui
	
	 Address:
 Attn:
Mr. Michael Hui
 Chief Executive Officer
 No. 3 Building, 720 Cailun Road
 Zhangjiang High Tech Park, Pu Dong New Area

Shanghai China

 
	
	SELLERS
	
	 /S/ Sofie Qiao

	 Shuang (Sofie) Qiao

	
	 /S/ Leonard Post

	 Leonard Post

	
	 /S/ Peter Myers

	 Peter Myers

	
	 /S/ Daniel Chu

	 Daniel Chu

	
	 /S/ Charles Hsu

	 Charles Hsu

	
	 /S/ Zhengying Pan

	 Zhengying Pan

	
	 /S/ Xiaoyi Xiao

	 Xiaoyi Xiao

	
	 /S/ David Hanabusa

	 David Hanabusa

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