human c-MET kinase domain complexed with 6-benzyloxyquinoline inhibitor

Experimental Data Snapshot

  • Resolution: 2.54 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 

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This is version 1.3 of the entry. See complete history


Discovery of 6-benzyloxyquinolines as c-Met selective kinase inhibitors

Nishii, H.Chiba, T.Morikami, K.Fukami, T.A.Sakamoto, H.Ko, K.Koyano, H.

(2010) Bioorg Med Chem Lett 20: 1405-1409

  • DOI: https://doi.org/10.1016/j.bmcl.2009.12.109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel quinoline derivative that selectively inhibits c-Met kinase was identified. The molecular design is based on a result of the analysis of a PF-2341066 (1)/c-Met cocrystal structure (PDB code: 2wgj). The kinase selectivity of the derivatives is discussed from the view point of the sequence homology of the kinases, the key interactions found in X-ray cocrystal structures, and the structure-activity relationship (SAR) obtained in this work.

  • Organizational Affiliation

    Department of Chemistry Research 2, Chugai Pharmaceutical Co, Ltd, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor319Homo sapiensMutation(s): 3 
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
Binding Affinity Annotations 
IDSourceBinding Affinity
DFQ PDBBind:  3A4P IC50: 28 (nM) from 1 assay(s)
BindingDB:  3A4P IC50: 28 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.54 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.227α = 90
b = 42.733β = 102.91
c = 46.039γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description