Crystal structure of D1228V c-MET bound by compound 16

Experimental Data Snapshot

  • Resolution: 2.21 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 

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Ligand Structure Quality Assessment 

This is version 1.2 of the entry. See complete history


Discovery and Optimization of the First ATP Competitive Type-III c-MET Inhibitor.

Michaelides, I.N.Collie, G.W.Borjesson, U.Vasalou, C.Alkhatib, O.Barlind, L.Cheung, T.Dale, I.L.Embrey, K.J.Hennessy, E.J.Khurana, P.Koh, C.M.Lamb, M.L.Liu, J.Moss, T.A.O'Neill, D.J.Phillips, C.Shaw, J.Snijder, A.Storer, R.I.Stubbs, C.J.Han, F.Li, C.Qiao, J.Sun, D.Q.Wang, J.Wang, P.Yang, W.

(2023) J Med Chem 66: 8782-8807

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c00401
  • Primary Citation of Related Structures:  
    8OUU, 8OUV, 8OV7, 8OVZ, 8OW3, 8OWG

  • PubMed Abstract: 

    Recent clinical reports have highlighted the need for wild-type (WT) and mutant dual inhibitors of c-MET kinase for the treatment of cancer. We report herein a novel chemical series of ATP competitive type-III inhibitors of WT and D1228V mutant c-MET. Using a combination of structure-based drug design and computational analyses, ligand 2 was optimized to a highly selective chemical series with nanomolar activities in biochemical and cellular settings. Representatives of the series demonstrate excellent pharmacokinetic profiles in rat in vivo studies with promising free-brain exposures, paving the way for the design of brain permeable drugs for the treatment of c-MET driven cancers.

  • Organizational Affiliation

    Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor
A, B
309Homo sapiensMutation(s): 1 
Gene Names: MET
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
PHAROS:  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
W3N (Subject of Investigation/LOI)
Query on W3N

Download Ideal Coordinates CCD File 
M [auth A],
W [auth B]
C22 H18 N6 O2
Query on IOD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.21 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.9α = 90
b = 56.67β = 90
c = 215.81γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2023-07-05 
  • Deposition Author(s): Collie, G.W.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-07-26
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Refinement description