7JV8 | pdb_00007jv8

Human CD73 (ecto 5'-nucleotidase) in complex with compound 35


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 
    0.279 (Depositor) 
  • R-Value Work: 
    0.220 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7JV8

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Orally Bioavailable Small-Molecule CD73 Inhibitor (OP-5244) Reverses Immunosuppression through Blockade of Adenosine Production.

Du, X.Moore, J.Blank, B.R.Eksterowicz, J.Sutimantanapi, D.Yuen, N.Metzger, T.Chan, B.Huang, T.Chen, X.Chen, Y.Duong, F.Kong, W.Chang, J.H.Sun, J.Zavorotinskaya, T.Ye, Q.Junttila, M.R.Ndubaku, C.Friedman, L.S.Fantin, V.R.Sun, D.

(2020) J Med Chem 63: 10433-10459

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c01086
  • Primary Citation Related Structures: 
    7JV8, 7JV9

  • PubMed Abstract: 

    The adenosinergic pathway represents an attractive new therapeutic approach in cancer immunotherapy. In this pathway, ecto-5-nucleotidase CD73 has the unique function of regulating production of immunosuppressive adenosine (ADO) through the hydrolysis of AMP. CD73 is overexpressed in many cancers, resulting in elevated levels of ADO that correspond to poor patient prognosis. Therefore, reducing the level of ADO via inhibition of CD73 is a potential strategy for treating cancers. Based on the binding mode of adenosine 5'-(α,β-methylene)diphosphate (AOPCP) with human CD73, we designed a series of novel monophosphonate small-molecule CD73 inhibitors. Among them, OP-5244 ( 35 ) proved to be a highly potent and orally bioavailable CD73 inhibitor. In preclinical studies, 35 completely inhibited ADO production in both human cancer cells and CD8 + T cells. Furthermore, 35 lowered the ratio of ADO/AMP significantly and reversed immunosuppression in mouse models, indicating its potential as an in vivo tool compound for further development.


  • Organizational Affiliation
    • ORIC Pharmaceuticals, 240 E. Grand Avenue, Floor 2, South San Francisco, California 94080, United States.

Macromolecule Content 

  • Total Structure Weight: 237.9 kDa 
  • Atom Count: 16,768 
  • Modeled Residue Count: 2,097 
  • Deposited Residue Count: 2,116 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5'-nucleotidase
A, B, C, D
529Homo sapiensMutation(s): 3 
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

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VPD
(Subject of Investigation/LOI)

Query on VPD



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
P [auth C],
T [auth D]
6-chloro-N-cyclopentyl-1-{5-O-[(2R)-1-hydroxy-3-methoxy-2-phosphonopropan-2-yl]-beta-D-ribofuranosyl}-1H-pyrazolo[3,4-d]pyrimidin-4-amine
C19 H29 Cl N5 O9 P
BQCRMLSBGAKPFW-RTPDKIPNSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
I [auth B]
J [auth B]
M [auth C]
E [auth A],
F [auth A],
I [auth B],
J [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
G [auth A],
K [auth B],
O [auth C],
S [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
VPD BindingDB:  7JV8 IC50: min: 0.25, max: 250 (nM) from 2 assay(s)
EC50: min: 0.22, max: 14 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free:  0.279 (Depositor) 
  • R-Value Work:  0.220 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.876α = 90
b = 102.354β = 103.22
c = 129.609γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary