Crystal structure of C-MET kinase domain in complex with N'-((3Z)-4- chloro-7-methyl-2-oxo-1,2-dihydro-3H-indol-3-ylidene)-2-(4- hydroxyphenyl)propanohydrazide

Experimental Data Snapshot

  • Resolution: 1.87 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

Starting Model: experimental
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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery of a Novel Class of Exquisitely Selective Mesenchymal-Epithelial Transition Factor (C-met) Protein Kinase Inhibitors and Identification of the Clinical Candidate 2-(4-(1-(Quinolin-6-Ylmethyl)-1H-[1,2, 3]Triazolo[4,5-B]Pyrazin-6-Yl)-1H-Pyrazol-1-Yl)Ethanol (Pf-04217903) for the Treatment of Cancer.

Cui, J.J.Mctigue, M.Nambu, M.Tran-Dube, M.Pairish, M.Shen, H.Jia, L.Cheng, H.Hoffman, J.Le, P.Jalaie, M.Goetz, G.H.Ryan, K.Grodsky, N.Deng, Y.Parker, M.Timofeevski, S.Murray, B.W.Yamazaki, S.Aguirre, S.Li, Q.Zou, H.Christensen, J.

(2012) J Med Chem 55: 8091

  • DOI: https://doi.org/10.1021/jm300967g
  • Primary Citation of Related Structures:  
    3ZXZ, 3ZZE, 4AOI, 4AP7

  • PubMed Abstract: 

    The c-MET receptor tyrosine kinase is an attractive oncology target because of its critical role in human oncogenesis and tumor progression. An oxindole hydrazide hit 6 was identified during a c-MET HTS campaign and subsequently demonstrated to have an unusual degree of selectivity against a broad array of other kinases. The cocrystal structure of the related oxindole hydrazide c-MET inhibitor 10 with a nonphosphorylated c-MET kinase domain revealed a unique binding mode associated with the exquisite selectivity profile. The chemically labile oxindole hydrazide scaffold was replaced with a chemically and metabolically stable triazolopyrazine scaffold using structure based drug design. Medicinal chemistry lead optimization produced 2-(4-(1-(quinolin-6-ylmethyl)-1H-[1,2,3]triazolo[4,5-b]pyrazin-6-yl)-1H-pyrazol-1-yl)ethanol (2, PF-04217903), an extremely potent and exquisitely selective c-MET inhibitor. 2 demonstrated effective tumor growth inhibition in c-MET dependent tumor models with good oral PK properties and an acceptable safety profile in preclinical studies. 2 progressed to clinical evaluation in a Phase I oncology setting.

  • Organizational Affiliation

    La Jolla Laboratories, Pfizer Worldwide Research and Development, 10770 Science Center Drive, San Diego, California 92121, USA. jean.cui@pfizer.com

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  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 6XP

Download Ideal Coordinates CCD File 
B [auth A](2S)-N'-[(3R)-4-chloro-7-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-2-(4-hydroxyphenyl)propanehydrazide
C18 H18 Cl N3 O3
Binding Affinity Annotations 
IDSourceBinding Affinity
6XP PDBBind:  3ZZE Ki: 1.3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.87 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.864α = 90
b = 94.373β = 90
c = 45.766γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-14
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references, Other, Structure summary
  • Version 1.2: 2012-10-10
    Changes: Database references
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description