3ZXZ

X-ray Structure of PF-04217903 bound to the kinase domain of c-Met


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HEPATOCYTE GROWTH FACTOR RECEPTOR
A
306Homo sapiensMutation(s): 0 
Gene Names: MET
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Go to Gene View: MET
Go to UniProtKB:  P08581
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KRW
Query on KRW

Download SDF File 
Download CCD File 
A
2-{4-[1-(QUINOLIN-6-YLMETHYL)-1H-[1,2,3]TRIAZOLO[4,5-B]PYRAZIN-6-YL]-1H-PYRAZOL-1-YL}ETHANOL
C19 H16 N8 O
PDMUGYOXRHVNMO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KRWIC50: 4 - 50 nM (99) BINDINGDB
KRWKi: 5 nM (99) BINDINGDB
KRWKi: 5 nM BINDINGMOAD
KRWKi: 4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 76.740α = 90.00
b = 94.125β = 90.00
c = 46.138γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CCP4phasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2012-09-26
    Type: Database references, Other, Structure summary
  • Version 1.2: 2012-10-10
    Type: Database references