3F82

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-MET in complex with N-(4-(2-amino-3-chloropyridin-4-yloxy)-3-fluorophenyl)-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.253 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 353Click on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

Discovery of N-(4-(2-Amino-3-chloropyridin-4-yloxy)-3-fluorophenyl)-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide (BMS-777607), a Selective and Orally Efficacious Inhibitor of the Met Kinase Superfamily

Schroeder, G.M.An, Y.Cai, Z.W.Chen, X.T.Clark, C.Cornelius, L.A.Dai, J.Gullo-Brown, J.Gupta, A.Henley, B.Hunt, J.T.Jeyaseelan, R.Kamath, A.Kim, K.Lippy, J.Lombardo, L.J.Manne, V.Oppenheimer, S.Sack, J.S.Schmidt, R.J.Shen, G.Stefanski, K.Tokarski, J.S.Trainor, G.L.Wautlet, B.S.Wei, D.Williams, D.K.Zhang, Y.Zhang, Y.Fargnoli, J.Borzilleri, R.M.

(2009) J Med Chem 52: 1251-1254

  • DOI: https://doi.org/10.1021/jm801586s
  • Primary Citation of Related Structures:  
    3F82

  • PubMed Abstract: 

    Substituted N-(4-(2-aminopyridin-4-yloxy)-3-fluoro-phenyl)-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamides were identified as potent and selective Met kinase inhibitors. Substitution of the pyridine 3-position gave improved enzyme potency, while substitution of the pyridone 4-position led to improved aqueous solubility and kinase selectivity. Analogue 10 demonstrated complete tumor stasis in a Met-dependent GTL-16 human gastric carcinoma xenograft model following oral administration. Because of its excellent in vivo efficacy and favorable pharmacokinetic and preclinical safety profiles, 10 has been advanced into phase I clinical trials.


  • Organizational Affiliation

    Bristol-Myers Squibb Research and Development, Princeton, New Jersey, 08543-4000, USA. gretchen.schroeder@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
hepatocyte growth factor receptor314Homo sapiensMutation(s): 3 
Gene Names: MET
EC: 2.7.10.1
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
353
Query on 353

Download Ideal Coordinates CCD File 
B [auth A]N-{4-[(2-amino-3-chloropyridin-4-yl)oxy]-3-fluorophenyl}-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1,2-dihydropyridine-3-carboxamide
C25 H19 Cl F2 N4 O4
VNBRGSXVFBYQNN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
353 BindingDB:  3F82 IC50: min: 2.5, max: 214 (nM) from 9 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.253 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.67α = 90
b = 46.883β = 90
c = 157.65γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTER-TNTrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 353Click on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2009-03-31 
  • Deposition Author(s): Sack, J.

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-10-20
    Changes: Database references
  • Version 1.3: 2023-12-27
    Changes: Data collection
  • Version 1.4: 2024-04-03
    Changes: Refinement description