2XP2

Structure of the Human Anaplastic Lymphoma Kinase in Complex with Crizotinib (PF-02341066)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
TYROSINE-PROTEIN KINASE RECEPTOR
A
327Homo sapiensMutation(s): 0 
Gene Names: ALK
EC: 2.7.10.1
Find proteins for Q9UM73 (Homo sapiens)
Go to UniProtKB:  Q9UM73
NIH Common Fund Data Resources
PHAROS  Q9UM73
Protein Feature View
  • Reference Sequence
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 %)
VGHIC50:  1.2000000476837158   nM  BindingDB
VGHKi:  0.7400000095367432   nM  BindingDB
VGHIC50:  1026   nM  BindingDB
VGHIC50:  51   nM  BindingDB
VGHIC50:  843   nM  BindingDB
VGHIC50:  2.9000000953674316   nM  BindingDB
VGHIC50:  7.400000095367432   nM  BindingDB
VGHIC50:  1148   nM  BindingDB
VGHIC50:  7.670000076293945   nM  BindingDB
VGHIC50:  5   nM  BindingDB
VGHIC50:  80   nM  BindingDB
VGHIC50:  478   nM  BindingDB
VGHIC50:  25   nM  BindingDB
VGHIC50:  17.600000381469727   nM  BindingDB
VGHEC50:  2042   nM  BindingDB
VGHIC50:  28   nM  BindingDB
VGHIC50:  17.299999237060547   nM  BindingDB
VGHIC50:  2   nM  BindingDB
VGHKi:  8.199999809265137   nM  BindingDB
VGHEC50:  22840   nM  BindingDB
VGHIC50:  36   nM  BindingDB
VGHIC50:  600   nM  BindingDB
VGHIC50:  605   nM  BindingDB
VGHIC50 :  1   nM  PDBBind
VGHIC50:  0.6399999856948853   nM  BindingDB
VGHIC50:  626   nM  BindingDB
VGHIC50:  2.700000047683716   nM  BindingDB
VGHKd:  4.400000095367432   nM  BindingDB
VGHIC50:  200   nM  BindingDB
VGHIC50:  220   nM  BindingDB
VGHIC50:  2.0999999046325684   nM  BindingDB
VGHIC50:  14   nM  BindingDB
VGHIC50:  337   nM  BindingDB
VGHKd:  3.5999999046325684   nM  BindingDB
VGHIC50:  24   nM  BindingDB
VGHIC50:  20   nM  BindingDB
VGHIC50:  1   nM  BindingDB
VGHIC50:  133   nM  BindingDB
VGHIC50:  1600   nM  BindingDB
VGHKd:  3.299999952316284   nM  BindingDB
VGHIC50:  110   nM  BindingDB
VGHEC50:  575   nM  BindingDB
VGHIC50:  188   nM  BindingDB
VGHIC50:  3039   nM  BindingDB
VGHIC50:  151   nM  BindingDB
VGHIC50:  165   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.633α = 90
b = 57.086β = 90
c = 104.709γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-09-28
    Changes: Database references, Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation