Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 72.71 kDa 
• Atom Count: 5303 
• Modelled Residue Count: 597 
• Deposited Residue Count: 636 
• Unique protein chains: 1

3RHK

Crystal structure of the catalytic domain of c-Met kinase in complex with ARQ 197

• DOI: 10.2210/pdb3RHK/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-11 Released: 2011-04-27 
• Deposition Author(s): Eathiraj, S., Palma, R., Volckova, E., Hirschi, M., France, D.S., Ashwell, M.A., Chan, T.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

Discovery of a novel mode of protein kinase inhibition characterized by the mechanism of inhibition of human mesenchymal-epithelial transition factor (c-Met) protein autophosphorylation by ARQ 197.

Eathiraj, S., Palma, R., Volckova, E., Hirschi, M., France, D.S., Ashwell, M.A., Chan, T.C.

(2011) J Biol Chem 286: 20666-20676

• PubMed: 21454604 
• DOI: 10.1074/jbc.M110.213801
• Primary Citation of Related Structures:  
  3RHK


• PubMed Abstract: 
  

A number of human malignancies exhibit sustained stimulation, mutation, or gene amplification of the receptor tyrosine kinase human mesenchymal-epithelial transition factor (c-Met). ARQ 197 is a clinically advanced, selective, orally bioavailable, and well tolerated c-Met inhibitor, currently in Phase 3 clinical testing in non-small cell lung cancer patients. Herein, we describe the molecular and structural basis by which ARQ 197 selectively targets c-Met. Through our analysis we reveal a previously undisclosed, novel inhibitory mechanism that utilizes distinct regulatory elements of the c-Met kinase. The structure of ARQ 197 in complex with the c-Met kinase domain shows that the inhibitor binds a conformation that is distinct from published kinase structures. ARQ 197 inhibits c-Met autophosphorylation and is highly selective for the inactive or unphosphorylated form of c-Met. Through our analysis of the interplay between the regulatory and catalytic residues of c-Met, and by comparison between the autoinhibited canonical conformation of c-Met bound by ARQ 197 to previously described kinase domains of type III receptor tyrosine kinases, we believe this to be the basis of a powerful new in silico approach for the design of similar inhibitors for other protein kinases of therapeutic interest.

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Organizational Affiliation: 

ArQule, Inc, Woburn, Massachusetts 01801, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, B	318	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M97	A, B	1-[(3R,4R)-4-(1H-indol-3-yl)-2,5-dioxopyrrolidin-3-yl]pyrrolo[3,2,1-ij]quinolinium C23 H16 N3 O2 DVSVKPFSHABFPS-PMACEKPBSA-O

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
M97	IC50 :  548   nM  PDBBind
M97	IC50:  520   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.254 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.47	α = 88.41
b = 58.67	β = 68.1
c = 64.96	γ = 85.52

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHARP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-04-11 
• Released Date: 2011-04-27 
Deposition Author(s): Eathiraj, S., Palma, R., Volckova, E., Hirschi, M., France, D.S., Ashwell, M.A., Chan, T.C.

Revision History  

• Version 1.0: 2011-04-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-28
  Changes: Database references