9I1H | pdb_00009i1h

Crystal structure of human CD73 (ecto-5'-nucleotidase) in complex with the AMPCP analog PSB-12730 in the closed state (crystal form IV)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 
    0.316 (Depositor), 0.319 (DCC) 
  • R-Value Work: 
    0.267 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 
    0.269 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Design, development and evaluation of a tritium-labeled radiotracer for ecto-5'-nucleotidase (CD73) - A versatile research tool and diagnostic agent for personalized medicine.

Idris, R.M.Al-Hroub, H.Schmies, C.C.Riziki, P.Renn, C.Claff, T.Sylvester, K.Moschutz, S.Reinhardt, J.Deuter-Conrad, W.Dietrich, J.M.Toma, M.Fleischmann, B.K.Wenzel, D.Zimmermann, H.Holzel, M.Strater, N.Muller, C.E.

(2025) Biomed Pharmacother 188: 118115-118115

  • DOI: https://doi.org/10.1016/j.biopha.2025.118115
  • Primary Citation of Related Structures:  
    9I1H

  • PubMed Abstract: 

    Ecto-5'-nucleotidase (CD73) is the main enzyme that catalyzes the hydrolysis of extracellular AMP to produce anti-inflammatory, immunosuppressive adenosine. Many tumor cells over-express ectonucleotidases accumulating adenosine in the tumor microenvironment, which promotes tumor growth, metastasis, angiogenesis, and immune escape. CD73 is upregulated in inflammation, and possesses potential as a biomarker and as a novel drug target for inflammatory diseases and cancer immunotherapy. New, metabolically stable N 6 -disubstituted adenosine-5'-diphosphate analogs were synthesized providing a basis for the design and preparation of the CD73-selective radioligand [ 3 H]PSB-17230 by catalytic hydrogenation of a propargyl-substituted precursor. It showed high, pico- to low nanomolar affinity for human, rat and mouse CD73, slow dissociation kinetics, negligible non-specific binding, and high selectivity, as confirmed by studies on an inactive CD73 mutant and CD73 knockout cells. A high-resolution co-crystal structure (2.35 Å) of PSB-17230 with human CD73 elucidated its binding interactions. Radioligand binding was employed to characterize competitive CD73 inhibitors and to study expression levels of the enzyme in tissues and tumor cell lines of different species. Moreover, [ 3 H]PSB-17230 was employed in autoradiography studies to determine CD73 expression in healthy and diseased mouse and human tissues. Significant upregulation of CD73 was observed in a mouse asthma model and in kidney cancer biopsies as compared to healthy controls. [ 3 H]PSB-17230 represents a high-affinity tracer which is anticipated to find broad application in drug screening, preclinical studies, and for diagnostic purposes in inflammation and cancer, enabling drug monitoring and targeted therapies.


  • Organizational Affiliation
    • PharmaCenter Bonn, Pharmaceutical Institute, Department of Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, Bonn D-53121, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-nucleotidase
A, B
567Homo sapiensMutation(s): 4 
Gene Names: NT5ENT5NTE
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21589
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free:  0.316 (Depositor), 0.319 (DCC) 
  • R-Value Work:  0.267 (Depositor), 0.267 (DCC) 
  • R-Value Observed: 0.269 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.168α = 90
b = 233.606β = 90
c = 54.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
autoBUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB 1328

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release