6TWA

Human CD73 (ecto 5'-nucleotidase) in complex with PSB12646 (an AOPCP derivative, compound 20 in publication) in the closed state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

2-Substituted alpha , beta-Methylene-ADP Derivatives: Potent Competitive Ecto-5'-nucleotidase (CD73) Inhibitors with Variable Binding Modes.

Bhattarai, S.Pippel, J.Scaletti, E.Idris, R.Freundlieb, M.Rolshoven, G.Renn, C.Lee, S.Y.Abdelrahman, A.Zimmermann, H.El-Tayeb, A.Muller, C.E.Strater, N.

(2020) J Med Chem 63: 2941-2957

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01611
  • Primary Citation of Related Structures:  
    6TVE, 6TVG, 6TVX, 6TW0, 6TWA, 6TWF

  • PubMed Abstract: 

    CD73 inhibitors are promising drugs for the (immuno)therapy of cancer. Here, we present the synthesis, structure-activity relationships, and cocrystal structures of novel derivatives of the competitive CD73 inhibitor α,β-methylene-ADP (AOPCP) substituted in the 2-position. Small polar or lipophilic residues increased potency, 2-iodo- and 2-chloro-adenosine-5'- O -[(phosphonomethyl)phosphonic acid] ( 15 , 16 ) being the most potent inhibitors with K i values toward human CD73 of 3-6 nM. Subject to the size and nature of the 2-substituent, variable binding modes were observed by X-ray crystallography. Depending on the binding mode, large species differences were found, e.g., 2-piperazinyl-AOPCP ( 21 ) was >12-fold less potent against rat CD73 compared to human CD73. This study shows that high CD73 inhibitory potency can be achieved by simply introducing a small substituent into the 2-position of AOPCP without the necessity of additional bulky N 6 -substituents. Moreover, it provides valuable insights into the binding modes of competitive CD73 inhibitors, representing an excellent basis for drug development.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-nucleotidase532Homo sapiensMutation(s): 5 
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: 2.00 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.938α = 90
b = 95.641β = 90
c = 233.642γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySTR 477/13-2

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary