Crystal structure of wild-type cMET bound by foretinib

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

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Structural and Molecular Insight into Resistance Mechanisms of First Generation cMET Inhibitors.

Collie, G.W.Koh, C.M.O'Neill, D.J.Stubbs, C.J.Khurana, P.Eddershaw, A.Snijder, A.Mauritzson, F.Barlind, L.Dale, I.L.Shaw, J.Phillips, C.Hennessy, E.J.Cheung, T.Narvaez, A.J.

(2019) ACS Med Chem Lett 10: 1322-1327

  • DOI: https://doi.org/10.1021/acsmedchemlett.9b00276
  • Primary Citation of Related Structures:  
    6SD9, 6SDC, 6SDD, 6SDE

  • PubMed Abstract: 

    Many small molecule inhibitors of the cMET receptor tyrosine kinase have been evaluated in clinical trials for the treatment of cancer and resistance-conferring mutations of cMET are beginning to be reported for a number of such compounds. There is now a need to understand specific cMET mutations at the molecular level, particularly concerning small molecule recognition. Toward this end, we report here the first crystal structures of the recent clinically observed resistance-conferring D1228V cMET mutant in complex with small molecule inhibitors, along with a crystal structure of wild-type cMET bound by the clinical compound savolitinib and supporting cellular, biochemical, and biophysical data. Our findings indicate that the D1228V alteration induces conformational changes in the kinase, which could have implications for small molecule inhibitor design. The data we report here increases our molecular understanding of the D1228V cMET mutation and provides insight for future inhibitor design.

  • Organizational Affiliation

    Discovery Sciences, R&D, AstraZeneca, Cambridge, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor309Homo sapiensMutation(s): 0 
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
88Z (Subject of Investigation/LOI)
Query on 88Z

Download Ideal Coordinates CCD File 
C [auth A]N-(3-fluoro-4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinolin-4-yl]oxy}phenyl)-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide
C34 H34 F2 N4 O6
Query on CL

Download Ideal Coordinates CCD File 
Binding Affinity Annotations 
IDSourceBinding Affinity
88Z BindingDB:  6SD9 IC50: min: 0.4, max: 214 (nM) from 22 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.88α = 90
b = 73.73β = 90
c = 91.47γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description