6Z9D

Human Ecto-5'-nucleotidase (CD73) in complex with AOPCP derivative AB680 (compound 55 in publication) in the closed form (crystal form III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of AB680: A Potent and Selective Inhibitor of CD73.

Lawson, K.V.Kalisiak, J.Lindsey, E.A.Newcomb, E.T.Leleti, M.R.Debien, L.Rosen, B.R.Miles, D.H.Sharif, E.U.Jeffrey, J.L.Tan, J.B.L.Chen, A.Zhao, S.Xu, G.Fu, L.Jin, L.Park, T.W.Berry, W.Moschutz, S.Scaletti, E.Strater, N.Walker, N.P.Young, S.W.Walters, M.J.Schindler, U.Powers, J.P.

(2020) J Med Chem 63: 11448-11468

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00525
  • Primary Citation of Related Structures:  
    6Z9B, 6Z9D

  • PubMed Abstract: 

    Extracellular adenosine (ADO), present in high concentrations in the tumor microenvironment (TME), suppresses immune function via inhibition of T cell and NK cell activation. Intratumoral generation of ADO depends on the sequential catabolism of ATP by two ecto-nucleotidases, CD39 (ATP → AMP) and CD73 (AMP → ADO). Inhibition of CD73 eliminates a major pathway of ADO production in the TME and can reverse ADO-mediated immune suppression. Extensive interrogation of structure-activity relationships (SARs), structure-based drug design, and optimization of pharmacokinetic properties culminated in the discovery of AB680, a highly potent ( K i = 5 pM), reversible, and selective inhibitor of CD73. AB680 is further characterized by very low clearance and long half-lives across preclinical species, resulting in a PK profile suitable for long-acting parenteral administration. AB680 is currently being evaluated in phase 1 clinical trials. Initial data show AB680 is well tolerated and exhibits a pharmacokinetic profile suitable for biweekly (Q2W) iv-administration in human.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
5'-nucleotidase557Homo sapiensMutation(s): 0 
Gene Names: NT5ENT5NTE
EC: 3.1.3.5
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QDH (Subject of Investigation/LOI)
Query on QDH

Download Ideal Coordinates CCD File 
E [auth A][[(2~{R},3~{S},4~{R},5~{R})-5-[6-chloranyl-4-[[(1~{S})-1-(2-fluorophenyl)ethyl]amino]pyrazolo[3,4-b]pyridin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic acid
C20 H24 Cl F N4 O9 P2
MFYLCAMJNGIULC-KCVUFLITSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QDH Binding MOAD:  6Z9D Ki: 5.00e-3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.214 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.226α = 90
b = 94.254β = 90
c = 235.428γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2020-09-16 
  • Deposition Author(s): Strater, N.

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description