2WGJ

X-ray Structure of PF-02341066 bound to the kinase domain of c-Met


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure Based Drug Design of Crizotinib (Pf-02341066), a Potent and Selective Dual Inhibitor of Mesenchymal-Epithelial Transition Factor (C-met) Kinase and Anaplastic Lymphoma Kinase (Alk).

Cui, J.J.Tran-Dube, M.Shen, H.Nambu, M.Kung, P.P.Pairish, M.Jia, L.Meng, J.Funk, L.Botrous, I.Mctigue, M.Grodsky, N.Ryan, K.Padrique, E.Alton, G.Timofeevski, S.Yamazaki, S.Li, Q.Zou, H.Christensen, J.Mroczkowski, B.Bender, S.Kania, R.S.Edwards, M.P.

(2011) J Med Chem 54: 6342

  • DOI: 10.1021/jm2007613
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Because of the critical roles of aberrant signaling in cancer, both c-MET and ALK receptor tyrosine kinases are attractive oncology targets for therapeutic intervention. The cocrystal structure of 3 (PHA-665752), bound to c-MET kinase domain, reveale ...

    Because of the critical roles of aberrant signaling in cancer, both c-MET and ALK receptor tyrosine kinases are attractive oncology targets for therapeutic intervention. The cocrystal structure of 3 (PHA-665752), bound to c-MET kinase domain, revealed a novel ATP site environment, which served as the target to guide parallel, multiattribute drug design. A novel 2-amino-5-aryl-3-benzyloxypyridine series was created to more effectively make the key interactions achieved with 3. In the novel series, the 2-aminopyridine core allowed a 3-benzyloxy group to reach into the same pocket as the 2,6-dichlorophenyl group of 3 via a more direct vector and thus with a better ligand efficiency (LE). Further optimization of the lead series generated the clinical candidate crizotinib (PF-02341066), which demonstrated potent in vitro and in vivo c-MET kinase and ALK inhibition, effective tumor growth inhibition, and good pharmaceutical properties.


    Organizational Affiliation

    La Jolla Laboratories, Pfizer Worldwide Research and Development, 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 UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS  P08581
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VGH
Query on VGH

Download CCD File 
A
3-[(1R)-1-(2,6-dichloro-3-fluorophenyl)ethoxy]-5-(1-piperidin-4-yl-1H-pyrazol-4-yl)pyridin-2-amine
C21 H22 Cl2 F N5 O
KTEIFNKAUNYNJU-GFCCVEGCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VGHKi:  2   nM  BindingDB
VGHIC50:  1   nM  BindingDB
VGHKd:  0.550000011920929   nM  BindingDB
VGHIC50:  7.099999904632568   nM  BindingDB
VGHIC50:  2   nM  BindingDB
VGHIC50:  14.600000381469727   nM  BindingDB
VGHKi:  19   nM  BindingDB
VGHIC50:  0.7799999713897705   nM  BindingDB
VGHKd:  1.5   nM  BindingDB
VGHIC50:  11   nM  BindingDB
VGHIC50:  2.4000000953674316   nM  BindingDB
VGHIC50:  18   nM  BindingDB
VGHIC50:  20   nM  BindingDB
VGHIC50:  16   nM  BindingDB
VGHIC50:  1.100000023841858   nM  BindingDB
VGHKi:  2   nM  Binding MOAD
VGHIC50:  1.399999976158142   nM  BindingDB
VGHIC50:  8   nM  BindingDB
VGHKd:  0.20000000298023224   nM  BindingDB
VGHKi:  4   nM  BindingDB
VGHKd:  2.0999999046325684   nM  BindingDB
VGHKi:  2   nM  PDBBind
VGHIC50:  1.600000023841858   nM  BindingDB
VGHIC50:  13.699999809265137   nM  BindingDB
VGHIC50:  4   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.926α = 90
b = 94.192β = 90
c = 45.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-06-02
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other