6XUQ | pdb_00006xuq

Human Ecto-5'-nucleotidase (CD73) in complex with A1618 (compound 1b in publication) in the closed state in crystal form III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 
    0.239 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.212 (Depositor) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Discovery of Potent and Selective Non-Nucleotide Small Molecule Inhibitors of CD73.

Beatty, J.W.Lindsey, E.A.Thomas-Tran, R.Debien, L.Mandal, D.Jeffrey, J.L.Tran, A.T.Fournier, J.Jacob, S.D.Yan, X.Drew, S.L.Ginn, E.Chen, A.Pham, A.T.Zhao, S.Jin, L.Young, S.W.Walker, N.P.Leleti, M.R.Moschutz, S.Strater, N.Powers, J.P.Lawson, K.V.

(2020) J Med Chem 63: 3935-3955

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01713
  • Primary Citation Related Structures: 
    6XUE, 6XUG, 6XUQ

  • PubMed Abstract: 

    CD73 is an extracellular mediator of purinergic signaling. When upregulated in the tumor microenvironment, CD73 has been implicated in the inhibition of immune function through overproduction of adenosine. Traditional efforts to inhibit CD73 have involved antibody therapy or the development of small molecules, the most potent of which mimic the acidic and ionizable structure of the enzyme's natural substrate, adenosine 5'-monophosphate (AMP). Here, we report the systematic discovery of a novel class of non-nucleotide CD73 inhibitors that are more potent than all other nonphosphonate inhibitor classes reported to date. These efforts have culminated in the discovery of 4-({5-[4-fluoro-1-(2 H -indazol-6-yl)-1 H -1,2,3-benzotriazol-6-yl]-1 H -pyrazol-1-yl}methyl)benzonitrile ( 73 , IC 50 = 12 nM) and 4-({5-[4-chloro-1-(2 H -indazol-6-yl)-1 H -1,2,3-benzotriazol-6-yl]-1 H -pyrazol-1-yl}methyl)benzonitrile ( 74 , IC 50 = 19 nM). Cocrystallization of 74 with human CD73 demonstrates a competitive binding mode. These compounds show promise for the improvement of drug-like character via the attenuation of the acidity and low membrane permeability inherent to known nucleoside inhibitors of CD73.


  • Organizational Affiliation
    • Arcus Biosciences, Inc., 3928 Point Eden Way, Hayward, California 94545, United States.

Macromolecule Content 

  • Total Structure Weight: 62.45 kDa 
  • Atom Count: 4,261 
  • Modeled Residue Count: 514 
  • Deposited Residue Count: 557 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5'-nucleotidase557Homo sapiensMutation(s): 0 
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

Binding Affinity Annotations 
IDSourceBinding Affinity
O1T BindingDB:  6XUQ IC50: min: 1.00e-2, max: 0.83 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free:  0.239 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.212 (Depositor) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.09α = 90
b = 93.85β = 90
c = 235.66γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACTdata extraction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-04-22 
  • Deposition Author(s): Strater, N.

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Structure summary
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Structure summary