3ZZE

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

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

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: 10.1021/jm300967g
  • Primary Citation of Related Structures:  
    4AP7, 4AOI, 3ZXZ, 3ZZE

  • 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 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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEPATOCYTE GROWTH FACTOR RECEPTOR A306Homo sapiensMutation(s): 0 
Gene Names: MET
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS:  P08581
GTEx:  ENSG00000105976
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6XP
Query on 6XP
Download Ideal Coordinates CCD File 
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
QYEVTRORXICGHU-VQVVDHBBSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6XPKi :  1.2999999523162842   nM  PDBBind
6XPKi:  1.2999999523162842   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

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