6XUG | pdb_00006xug

Human Ecto-5'-nucleotidase (CD73) in complex with A2410 (compound 53 in publication) in the closed form in crystal form IV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 
    0.237 (Depositor), 0.262 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6XUG

Ligand Structure Quality Assessment 


This is version 2.2 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: 120.27 kDa 
  • Atom Count: 8,965 
  • Modeled Residue Count: 1,029 
  • Deposited Residue Count: 1,076 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
5'-nucleotidase
A, B
538Homo 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

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O1Q
(Subject of Investigation/LOI)

Query on O1Q



Download:Ideal Coordinates CCD File
G [auth A],
L [auth B]
4-chloranyl-1-(1~{H}-indazol-6-yl)-6-[2-(3-methylphenyl)pyrazol-3-yl]benzotriazole
C23 H16 Cl N7
CSVTXOXVXICQEG-UHFFFAOYSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
F [auth A],
K [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN

Query on ZN



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
H [auth B],
I [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free:  0.237 (Depositor), 0.262 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.75α = 90
b = 230.01β = 90
c = 54.27γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
autoBUSTERphasing

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 2.0: 2020-09-23
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 2.2: 2024-11-06
    Changes: Structure summary