Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.33 kDa 
• Atom Count: 2,519 
• Modelled Residue Count: 290 
• Deposited Residue Count: 306 
• Unique protein chains: 1

 2WGJ

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

• PDB DOI:  https://doi.org/10.2210/pdb2WGJ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-04-20 Released: 2009-06-02 
• Deposition Author(s): McTigue, M., Grodsky, N., Ryan, K., Tran-Dube, M., Cui, J.J., Mroczkowski, B.

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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 

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

• PubMed: 21812414 
• DOI: https://doi.org/10.1021/jm2007613
• Primary Citation of Related Structures:  
  2WGJ, 2WKM, 2XP2


• 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, 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.

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Organizational Affiliation: 

La Jolla Laboratories, Pfizer Worldwide Research and Development, San Diego, California 92121, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR RECEPTOR	A	306	Homo sapiens	Mutation(s): 0  Gene Names: MET EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
PHAROS:  P08581

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VGH	B [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
VGH	BindingDB:  2WGJ	Ki: min: 2, max: 19 (nM) from 3 assay(s)
		Kd: min: 0.2, max: 2.1 (nM) from 5 assay(s)
		IC50: min: 0.51, max: 20 (nM) from 23 assay(s)
	Binding MOAD:  2WGJ	Ki: 2 (nM) from 1 assay(s)
	PDBBind:  2WGJ	Ki: 2 (nM) from 1 assay(s)

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 = 76.926	α = 90
b = 94.192	β = 90
c = 45.99	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-02 
Deposition Author(s): McTigue, M., Grodsky, N., Ryan, K., Tran-Dube, M., Cui, J.J., Mroczkowski, B.

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