9HJ4 | pdb_00009hj4

Crystal structure of CD73 (ecto-5'-nucleotidase) complexed to 8-butylthioadenosine 5'monophosphate (compound 3 in publication) in the open enzyme state

• PDB DOI: https://doi.org/10.2210/pdb9HJ4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2024-11-27 Released: 2025-05-28 
• Deposition Author(s): Strater, N., Moschuetz, S., Bi, C., Muller, C.E.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free: 
  0.148 (Depositor), 0.149 (DCC) 
• R-Value Work: 
  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 
  0.131 (Depositor) 

Starting Model: experimental

Literature

Synthesis, Characterization, Interactions, and Immunomodulatory Function of Ectonucleotidase CD39/CD73 Inhibitor 8-Butylthioadenosine 5'-Monophosphate.

Bi, C., Mirza, S., Baburi, H., Schakel, L., Winzer, R., Moschutz, S., Keetz, K., Lopez, V., Pelletier, J., Sevigny, J., Schulze Zur Wiesch, J., Claff, T., Tolosa, E., Namasivayam, V., Strater, N., Muller, C.E.

(2025) Acs Pharmacol Transl Sci 8: 1401-1415

• PubMed: 40370983 
• DOI: https://doi.org/10.1021/acsptsci.5c00126
• Primary Citation of Related Structures:  
  9HJ4


• PubMed Abstract: 
  

  Ectonucleoside triphosphate diphosphohydrolase-1 (NTPDase1, CD39) catalyzes the extracellular hydrolysis of ATP generating AMP, while ecto-5'-nucleotidase (CD73) further hydrolyzes AMP yielding immunosuppressive adenosine. 8-Butylthioadenosine 5'-monophosphate (8-BuS-AMP) was described as a CD39 inhibitor but has been poorly characterized. The standard CD39 antagonist ARL 67156 is not suitable for in vivo studies due to metabolic instability. In the present study, we optimized and upscaled the synthesis of 8-BuS-AMP and performed a comprehensive investigation of its properties. It behaves as a competitive inhibitor at human and mouse CD39, and additionally inhibits CD73. Docking studies using a homology model of human CD39 and determination of an atomic-resolution (1.06 Å) cocrystal structure with human CD73 indicated the inhibitor's interactions within the substrate binding pockets and explained the compound's stability toward hydrolysis. 8-BuS-AMP is metabolically highly stable in human and mouse liver microsomes. It inhibited ε-adenosine formation from ε-ATP and ε-AMP in human synovial fluid and enhanced activation and proliferation of peripheral human T lymphocytes. Thus, 8-BuS-AMP is a recommended tool compound for studying purinergic signaling in vitro and in vivo, being superior to the standard CD39 inhibitor ARL 67156. Moreover, it may serve as a lead structure to develop drugs for the immunotherapy of cancer.

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Organizational Affiliation: 
• PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany.
Department of Immunology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, 04103 Leipzig, Germany.
Department of Internal Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, Hamburg 100020, Germany.
Centre de Recherche du CHU de Québec - Université Laval, Québec City, Quebec G1 V 4G2, Canada.
Départment de Microbiologie-Infectiologie et d'Immunologie, Faculté de Médecine, Université Laval, Quebec City, Quebec G1 V 0A6, Canada.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.36 kDa 
• Atom Count: 5,097 
• Modeled Residue Count: 523 
• Deposited Residue Count: 547 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-nucleotidase	A	547	Homo sapiens	Mutation(s): 4  Gene Names: NT5E, NT5, NTE EC: 3.1.3.5 (PDB Primary Data), 3.1.3.99 (UniProt), 3.1.3.89 (UniProt), 3.1.3.35 (UniProt), 3.1.3.91 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21589 (Homo sapiens) Explore P21589  Go to UniProtKB:  P21589
PHAROS:  P21589 GTEx:  ENSG00000135318

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1IVB (Subject of Investigation/LOI)	E [auth A]	[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-butylsulfanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate C14 H22 N5 O7 P S VFLYSLPYKLFYSL-QYVSTXNMSA-N
1PE	F [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
PGE	G [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.06 Å
• R-Value Free:  0.148 (Depositor), 0.149 (DCC) 
• R-Value Work:  0.130 (Depositor), 0.131 (DCC) 
• R-Value Observed: 0.131 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.251	α = 90
b = 131.045	β = 90
c = 66.351	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
STARANISO	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Strater, N., Moschuetz, S., Bi, C., Muller, C.E.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	335447717

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release