Document:

EX-4.7

 EXHIBIT 4.7 

SECOND SUPPLEMENTAL INDENTURE 

Dated as of May 22, 2022 
 to 

Indenture dated as of February 4, 2020 

THIS SECOND SUPPLEMENTAL INDENTURE (this “Second Supplemental
Indenture”), dated as of May 22, 2022, among UNEV Pipeline, LLC, a Delaware limited liability company (the “Guaranteeing Subsidiary”), Holly Energy Partners, L.P., a Delaware limited partnership
(“Holly Energy Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and collectively with Holly Energy Partners, the “Issuers”), the other Guarantors (as defined in the
Indenture referred to herein) and U.S. Bank Trust Company, National Association (successor in interest to U.S. Bank National Association), as trustee under the Indenture referred to herein (the “Trustee”). 

W I T N E S S E T H 
 WHEREAS,
the Issuers have heretofore executed and delivered to the Trustee an indenture (the “Indenture”), dated as of February 4, 2020, providing for the issuance of 5.000% Senior Notes due 2028 (the
“Notes”), and a first supplemental indenture, dated March 14, 2022, providing for the addition of Sinclair Transportation Company LLC, a Wyoming limited liability company, Sinclair Logistics, LLC, a Wyoming limited
liability company, and Sinclair Pipeline Company, LLC, a Wyoming limited liability company, each as a Guarantor under the Indenture; 

WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiary shall execute and deliver to the Trustee a
supplemental indenture pursuant to which the Guaranteeing Subsidiary shall unconditionally guarantee all of the Issuers’ Obligations under the Notes and the Indenture on the terms and conditions set forth therein (the “Note
Guarantee”); and 
 WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is authorized to execute and deliver
this Second Supplemental Indenture. 
 NOW, THEREFORE, in consideration of the foregoing and for other good and valuable consideration, the
receipt of which is hereby acknowledged, the Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows: 

1.    CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the
meanings assigned to them in the Indenture. 
 2.    AGREEMENT TO
GUARANTEE. The Guaranteeing Subsidiary hereby agrees to provide a Guarantee on the terms and subject to the conditions set forth in the Indenture including but not limited to Article 10 thereof. 

 3.    NO RECOURSE AGAINST
OTHERS. No past, present or future director, officer, partner, member, employee, incorporator, manager, unit holder or other owner of an Equity Interest of the Guaranteeing Subsidiary, as such, shall have any liability for any
obligations of the Issuers or the Guarantors under the Notes, any Note Guarantees, the Indenture or this Second Supplemental Indenture or for any claim based on, in respect of, or by reason of, such obligations or their creation. Each Holder of the
Notes by accepting a Note waives and releases all such liability. The waiver and release are part of the consideration for issuance of the Notes and the Note Guarantees. 

4.    NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL GOVERN AND BE USED TO CONSTRUE THIS SECOND
SUPPLEMENTAL INDENTURE. 
 5.    COUNTERPARTS. The parties may sign any number of copies of this Second
Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement. 

6.    EFFECT OF HEADINGS. The Section headings herein are for convenience
only and shall not affect the construction hereof. 
 7.    THE TRUSTEE. The Trustee shall
not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this Second Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing
Subsidiary and the Issuers. 
 [Remainder of Page Intentionally Left Blank] 

  
 2 

 IN WITNESS WHEREOF, the parties hereto have caused this Second Supplemental Indenture to be
duly executed and attested, all as of the date first above written. 
  

			
	GUARANTEEING SUBSIDIARY:
	
	UNEV PIPELINE, LLC, a Delaware limited liability company
		
	By:	 	/s/ John Harrison
		 	 John Harrison
 Vice President, Finance,
Strategy and
 Treasurer

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
							
	ISSUERS:
	
	HOLLY ENERGY PARTNERS, L.P.
		
	By:	 	 HEP Logistic Holdings, L.P.,
 its
general partner

			
		 	By:	 	Holly Logistic Services, L.L.C., its general partner
				
		 		 	By:	 	/s/ John Harrison
		 		 		 	 John Harrison
 Senior Vice President, Chief
Financial
 Officer and Treasurer

  

			
	HOLLY ENERGY FINANCE CORP.
		
	By:	 	/s/ John Harrison
		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
	
	OTHER GUARANTORS:
	
	CHEYENNE LOGISTICS LLC, a Delaware limited liability company
	
	EL DORADO LOGISTICS LLC, a Delaware limited liability company
	
	EL DORADO OPERATING LLC, a Delaware limited liability company
	
	EL DORADO OSAGE LLC, a Delaware limited liability company
	
	FRONTIER ASPEN LLC, a Delaware limited liability company
	
	HEP CHEYENNE LLC, a Delaware limited liability company
	
	HEP CUSHING LLC, a Delaware limited liability company
	
	HEP EL DORADO LLC, a Delaware limited liability company
	
	HEP LOGISTICS GP, L.L.C., a Delaware limited liability company
	
	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability company
	
	HEP OKLAHOMA, LLC, a Delaware limited liability company
	
	HEP PIPELINE, L.L.C., a Delaware limited liability company
	
	HEP PIPELINE GP, L.L.C., a Delaware limited liability company
	
	HEP REFINING, L.L.C., a Delaware limited liability company
	
	HEP REFINING GP, L.L.C., a Delaware limited liability company

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
	
	HEP TULSA LLC, a Delaware limited liability company
	
	HEP UNEV HOLDINGS LLC, a Delaware limited liability company
	
	HEP UNEV PIPELINE LLC, a Delaware limited liability company
	
	HEP WOODS CROSS, L.L.C., a Delaware limited liability company
	
	HOLLY ENERGY HOLDINGS LLC, a Delaware limited liability company
	
	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited liability company
	
	LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability company
	
	ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability company
	
	SLC PIPELINE LLC, a Delaware limited liability company
	
	WOODS CROSS OPERATING LLC, a Delaware limited liability company
	
	SINCLAIR TRANSPORTATION COMPANY LLC, a Wyoming limited liability company

  

			
	By:	 	/s/ John Harrison
		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
	
	HEP FIN-TEX/TRUST RIVER, L.P., a Texas limited partnership
	
	HEP NAVAJO SOUTHERN, L.P., a Delaware limited partnership
	
	HEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware limited partnership

  

					
	Each by:	 	HEP Pipeline GP, L.L.C., a Delaware limited liability company, its General Partner
			
		 	By:	 	/s/ John Harrison
		 		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  

					
	HEP REFINING ASSETS, L.P., a Delaware limited partnership
		
	By:	 	HEP Refining GP, L.L.C., a Delaware limited liability company, its General Partner
			
		 	By:	 	/s/ John Harrison
		 		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  

					
	HOLLY ENERGY PARTNERS—OPERATING, L.P., a Delaware limited partnership
		
	By:	 	HEP Logistics GP, L.L.C., a Delaware limited liability company, its General Partner
			
		 	By:	 	/s/ John Harrison
		 		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
					
	SINCLAIR LOGISTICS, LLC, a Wyoming limited liability company
	
	SINCLAIR PIPELINE COMPANY, LLC, a Wyoming limited liability company
		
	By:	 	Sinclair Transportation Company LLC, a Wyoming limited liability company, its Sole Member
			
		 	By:	 	/s/ John Harrison
		 		 	 John Harrison
 Senior Vice President, Chief
Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTURE 

 
			
	U.S. BANK TRUST COMPANY, NATIONAL ASSOCIATION, as Trustee
		
	By:	 	/s/ Michael K. Herberger
	Name:	 	Michael K. Herberger
	Title:	 	Vice President

  
 SIGNATURE
PAGE TO SECOND SUPPLEMENTAL INDENTUREEX-4.9

 EXHIBIT 4.9 

FIRST SUPPLEMENTAL INDENTURE 

Dated as of May 22, 2022 
 to 

Indenture dated as of April 8, 2022 

THIS FIRST SUPPLEMENTAL INDENTURE (this “First Supplemental
Indenture”), dated as of May 22, 2022, among UNEV Pipeline, LLC, a Delaware limited liability company (the “Guaranteeing Subsidiary”), Holly Energy Partners, L.P., a Delaware limited partnership
(“Holly Energy Partners”), and Holly Energy Finance Corp. (“Finance Corp.” and collectively with Holly Energy Partners, the “Issuers”), the other Guarantors (as defined in the
Indenture referred to herein) and U.S. Bank Trust Company, National Association, as trustee under the Indenture referred to herein (the “Trustee”). 

W I T N E S S E T H 
 WHEREAS,
the Issuers have heretofore executed and delivered to the Trustee an indenture (the “Indenture”), dated as of April 8, 2022, providing for the issuance of 6.375% Senior Notes due 2027 (the
“Notes”); 
 WHEREAS, the Indenture provides that under certain circumstances the Guaranteeing Subsidiary shall
execute and deliver to the Trustee a supplemental indenture pursuant to which the Guaranteeing Subsidiary shall unconditionally guarantee all of the Issuers’ Obligations under the Notes and the Indenture on the terms and conditions set forth
therein (the “Note Guarantee”); and 
 WHEREAS, pursuant to Section 9.01 of the Indenture, the Trustee is
authorized to execute and deliver this First Supplemental Indenture. 
 NOW, THEREFORE, in consideration of the foregoing and for other good
and valuable consideration, the receipt of which is hereby acknowledged, the Guaranteeing Subsidiary and the Trustee mutually covenant and agree for the equal and ratable benefit of the Holders of the Notes as follows: 

1.    CAPITALIZED TERMS. Capitalized terms used herein without definition shall have the
meanings assigned to them in the Indenture. 
 2.    AGREEMENT TO
GUARANTEE. The Guaranteeing Subsidiary hereby agrees to provide a Guarantee on the terms and subject to the conditions set forth in the Indenture including but not limited to Article 10 thereof. 

3.    NO RECOURSE AGAINST OTHERS. No past, present or future
director, officer, partner, member, employee, incorporator, manager, unit holder or other owner of an Equity Interest of the Guaranteeing Subsidiary, as such, shall have any liability for any obligations of the Issuers or the Guarantors under the
Notes, any Note Guarantees, the Indenture or this First Supplemental Indenture or for any claim based on, in respect of, or by reason of, such obligations or their creation. Each Holder of the Notes by accepting a Note waives and releases all such
liability. The waiver and release are part of the consideration for issuance of the Notes and the Note Guarantees. 

 4.    NEW YORK LAW TO GOVERN. THE LAW OF THE STATE OF NEW YORK SHALL
GOVERN AND BE USED TO CONSTRUE THIS FIRST SUPPLEMENTAL INDENTURE. 
 5.    COUNTERPARTS. The parties may
sign any number of copies of this First Supplemental Indenture. Each signed copy shall be an original, but all of them together represent the same agreement. 

6.    EFFECT OF HEADINGS. The Section headings herein are for convenience
only and shall not affect the construction hereof. 
 7.    THE TRUSTEE. The Trustee shall
not be responsible in any manner whatsoever for or in respect of the validity or sufficiency of this First Supplemental Indenture or for or in respect of the recitals contained herein, all of which recitals are made solely by the Guaranteeing
Subsidiary and the Issuers. 
 [Remainder of Page Intentionally Left Blank] 

  
 2 

 IN WITNESS WHEREOF, the parties hereto have caused this First Supplemental Indenture to be
duly executed and attested, all as of the date first above written. 
  

			
	GUARANTEEING SUBSIDIARY:
	
	UNEV PIPELINE, LLC, a Delaware limited liability company
		
	By:	 	 /s/ John Harrison

		 	John Harrison
		 	Vice President, Finance, Strategy and Treasurer

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

 
							
	ISSUERS:
	
	HOLLY ENERGY PARTNERS, L.P.
		
	By:	 	HEP Logistic Holdings, L.P., its general partner
			
		 	By:	 	Holly Logistic Services, L.L.C., its general partner
				
		 		 	By:	 	 /s/ John Harrison 

		 		 		 	John Harrison
		 		 		 	Senior Vice President, Chief Financial Officer and Treasurer
	
	HOLLY ENERGY FINANCE CORP.
		
	By:	 	 /s/ John Harrison

		 	John Harrison
		 	Senior Vice President, Chief Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

 
			
	OTHER GUARANTORS:
	
	CHEYENNE LOGISTICS LLC, a Delaware limited liability company
	
	EL DORADO LOGISTICS LLC, a Delaware limited liability company
	
	EL DORADO OPERATING LLC, a Delaware limited liability company
	
	EL DORADO OSAGE LLC, a Delaware limited liability company
	
	FRONTIER ASPEN LLC, a Delaware limited liability company
	
	HEP CHEYENNE LLC, a Delaware limited liability company
	
	HEP CUSHING LLC, a Delaware limited liability company
	
	HEP EL DORADO LLC, a Delaware limited liability company
	
	HEP LOGISTICS GP, L.L.C., a Delaware limited liability company
	
	HEP MOUNTAIN HOME, L.L.C., a Delaware limited liability company
	
	HEP OKLAHOMA, LLC, a Delaware limited liability company
	
	HEP PIPELINE, L.L.C., a Delaware limited liability company
	
	HEP PIPELINE GP, L.L.C., a Delaware limited liability company
	
	HEP REFINING, L.L.C., a Delaware limited liability company
	
	HEP REFINING GP, L.L.C., a Delaware limited liability company

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

			
	HEP TULSA LLC, a Delaware limited liability company
	
	HEP UNEV HOLDINGS LLC, a Delaware limited liability company
	
	HEP UNEV PIPELINE LLC, a Delaware limited liability company
	
	HEP WOODS CROSS, L.L.C., a Delaware limited liability company
	
	HOLLY ENERGY HOLDINGS LLC, a Delaware limited liability company
	
	HOLLY ENERGY STORAGE-LOVINGTON LLC, a Delaware limited liability company
	
	LOVINGTON-ARTESIA, L.L.C., a Delaware limited liability company
	
	ROADRUNNER PIPELINE, L.L.C., a Delaware limited liability company
	
	SLC PIPELINE LLC, a Delaware limited liability company
	
	WOODS CROSS OPERATING LLC, a Delaware limited liability company
	
	SINCLAIR TRANSPORTATION COMPANY LLC, a Wyoming limited liability company
		
	By:	 	 /s/ John Harrison

		 	John Harrison
		 	Senior Vice President, Chief Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

 
							
	HEP FIN-TEX/TRUST RIVER, L.P., a Texas limited partnership
	
	HEP NAVAJO SOUTHERN, L.P., a Delaware limited partnership
	
	HEP PIPELINE ASSETS, LIMITED PARTNERSHIP, a Delaware limited partnership
		
	Each by:	 	HEP Pipeline GP, L.L.C., a Delaware limited liability company, its General Partner
				
	 	 	 	 	By:	 	 /s/ John Harrison

		 		 		 	John Harrison
		 		 		 	Senior Vice President, Chief Financial Officer and Treasurer
	
	HEP REFINING ASSETS, L.P., a Delaware limited partnership
		
	By:	 	HEP Refining GP, L.L.C., a Delaware limited liability company, its General Partner
			
		 	By:	 	 /s/ John Harrison

		 		 	John Harrison
		 		 	Senior Vice President, Chief Financial Officer and Treasurer
	
	HOLLY ENERGY PARTNERS—OPERATING, L.P., a Delaware limited partnership
		
	By:	 	HEP Logistics GP, L.L.C., a Delaware limited liability company, its General Partner
			
		 	By:	 	 /s/ John Harrison 

		 		 	John Harrison
		 		 	Senior Vice President, Chief Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

 
					
	SINCLAIR LOGISTICS, LLC, a Wyoming limited liability company
	
	SINCLAIR PIPELINE COMPANY, LLC, a Wyoming limited liability company
		
	By:	 	Sinclair Transportation Company LLC, a Wyoming limited liability company, its Sole Member
			
		 	By:	 	 /s/ John Harrison 

		 		 	John Harrison
		 		 	Senior Vice President, Chief Financial Officer and Treasurer

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE 

 
			
	U.S. BANK TRUST COMPANY, NATIONAL ASSOCIATION, as Trustee
		
	By:	 	 /s/ Michael K. Herberger

	Name:	 	Michael K. Herberger
	Title:	 	Vice President

  
 SIGNATURE
PAGE TO FIRST SUPPLEMENTAL INDENTURE

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