Crystal structure of c-Met in complex with naphthyridinone inhibitor 5

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Discovery of (R)-6-(1-(8-Fluoro-6-(1-methyl-1H-pyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl)ethyl)-3-(2-methoxyethoxy)-1,6-naphthyridin-5(6H)-one (AMG 337), a Potent and Selective Inhibitor of MET with High Unbound Target Coverage and Robust In Vivo Antitumor Activity.

Boezio, A.A.Copeland, K.W.Rex, K.K Albrecht, B.Bauer, D.Bellon, S.F.Boezio, C.Broome, M.A.Choquette, D.Coxon, A.Dussault, I.Hirai, S.Lewis, R.Lin, M.H.Lohman, J.Liu, J.Peterson, E.A.Potashman, M.Shimanovich, R.Teffera, Y.Whittington, D.A.Vaida, K.R.Harmange, J.C.

(2016) J Med Chem 59: 2328-2342

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01716
  • Primary Citation of Related Structures:  
    5EYC, 5EYD

  • PubMed Abstract: 

    Deregulation of the receptor tyrosine kinase mesenchymal epithelial transition factor (MET) has been implicated in several human cancers and is an attractive target for small molecule drug discovery. Herein, we report the discovery of compound 23 (AMG 337), which demonstrates nanomolar inhibition of MET kinase activity, desirable preclinical pharmacokinetics, significant inhibition of MET phosphorylation in mice, and robust tumor growth inhibition in a MET-dependent mouse efficacy model.

  • Organizational Affiliation

    Amgen Incorporated , One Amgen Center Drive, Thousand Oaks, California 91320, United States.

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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5SZ

Download Ideal Coordinates CCD File 
B [auth A]6-[(1~{R})-1-[8-fluoranyl-6-(3-methyl-1,2-oxazol-5-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl]-1,6-naphthyridin-5-one
C20 H15 F N6 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
5SZ BindingDB:  5EYC IC50: min: 3, max: 9 (nM) from 2 assay(s)
Binding MOAD:  5EYC IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.073α = 90
b = 43.267β = 90
c = 158.02γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
CrystalCleardata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2016-04-06
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description