Crystal structure of c-MET bound by compound 4

Experimental Data Snapshot

  • Resolution: 2.02 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

Starting Model: other
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structural Basis for Targeting the Folded P-Loop Conformation of c-MET.

Collie, G.W.Michaelides, I.N.Embrey, K.Stubbs, C.J.Borjesson, U.Dale, I.L.Snijder, A.Barlind, L.Song, K.Khurana, P.Phillips, C.Storer, R.I.

(2021) ACS Med Chem Lett 12: 162-167

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00392
  • Primary Citation of Related Structures:  
    7B3Q, 7B3T, 7B3V, 7B3W, 7B3Z, 7B40, 7B41, 7B42, 7B43, 7B44

  • PubMed Abstract: 

    We report here a fragment screen directed toward the c-MET kinase from which we discovered a series of inhibitors able to bind to a rare conformation of the protein in which the P-loop adopts a collapsed, or folded, arrangement. Preliminary SAR exploration led to an inhibitor ( 7 ) with nanomolar biochemical activity against c-MET and promising cell activity and kinase selectivity. These findings increase our structural understanding of the folded P-loop conformation of c-MET and provide a sound structural and chemical basis for further investigation of this underexplored yet potentially therapeutically exploitable conformational state.

  • Organizational Affiliation

    Discovery Sciences, R&D, AstraZeneca, Cambridge, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor299Homo sapiensMutation(s): 0 
Gene Names: MET
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
GTEx:  ENSG00000105976 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SVH (Subject of Investigation/LOI)
Query on SVH

Download Ideal Coordinates CCD File 
C [auth A]3-(6-fluoranyl-1~{H}-indazol-4-yl)-4,5-dihydro-1~{H}-pyrrolo[3,4-b]pyrrol-6-one
C13 H9 F N4 O
Query on EDO

Download Ideal Coordinates CCD File 
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 2.02 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.82α = 90
b = 66.82β = 90
c = 188.63γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2020-12-09 
  • Deposition Author(s): Collie, G.W.

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-09
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-02-03
    Changes: Database references
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description