3RHK

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M110.213801

  • 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, an ...

    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.


    Organizational Affiliation

    ArQule, Inc, Woburn, Massachusetts 01801, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatocyte growth factor receptor
A, B
318Homo 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
M97
Query on M97

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
M97IC50: 520 nM BINDINGMOAD
M97IC50: 548 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.200 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.470α = 88.41
b = 58.670β = 68.10
c = 64.960γ = 85.52
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALAdata scaling
HKL-2000data collection
REFMACrefinement
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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