3DKG

Structure of Mutant(Y1248L) MET receptor tyrosine kinase in complex with inhibitor SGX-523


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SGX523 is an exquisitely selective, ATP-competitive inhibitor of the MET receptor tyrosine kinase with antitumor activity in vivo.

Buchanan, S.G.Hendle, J.Lee, P.S.Smith, C.R.Bounaud, P.Y.Jessen, K.A.Tang, C.M.Huser, N.H.Felce, J.D.Froning, K.J.Peterman, M.C.Aubol, B.E.Gessert, S.F.Sauder, J.M.Schwinn, K.D.Russell, M.Rooney, I.A.Adams, J.Leon, B.C.Do, T.H.Blaney, J.M.Sprengeler, P.A.Thompson, D.A.Smyth, L.Pelletier, L.A.Atwell, S.Holme, K.Wasserman, S.R.Emtage, S.Burley, S.K.Reich, S.H.

(2009) Mol Cancer Ther 8: 3181-3190

  • DOI: 10.1158/1535-7163.MCT-09-0477
  • Primary Citation of Related Structures:  
    3DKC, 3DKF, 3DKG

  • PubMed Abstract: 
  • The MET receptor tyrosine kinase has emerged as an important target for the development of novel cancer therapeutics. Activation of MET by mutation or gene amplification has been linked to kidney, gastric, and lung cancers. In other cancers, such as ...

    The MET receptor tyrosine kinase has emerged as an important target for the development of novel cancer therapeutics. Activation of MET by mutation or gene amplification has been linked to kidney, gastric, and lung cancers. In other cancers, such as glioblastoma, autocrine activation of MET has been demonstrated. Several classes of ATP-competitive inhibitor have been described, which inhibit MET but also other kinases. Here, we describe SGX523, a novel, ATP-competitive kinase inhibitor remarkable for its exquisite selectivity for MET. SGX523 potently inhibited MET with an IC50 of 4 nmol/L and is >1,000-fold selective versus the >200-fold selectivity of other protein kinases tested in biochemical assays. Crystallographic study revealed that SGX523 stabilizes MET in a unique inactive conformation that is inaccessible to other protein kinases, suggesting an explanation for the selectivity. SGX523 inhibited MET-mediated signaling, cell proliferation, and cell migration at nanomolar concentrations but had no effect on signaling dependent on other protein kinases, including the closely related RON, even at micromolar concentrations. SGX523 inhibition of MET in vivo was associated with the dose-dependent inhibition of growth of tumor xenografts derived from human glioblastoma and lung and gastric cancers, confirming the dependence of these tumors on MET catalytic activity. Our results show that SGX523 is the most selective inhibitor of MET catalytic activity described to date and is thus a useful tool to investigate the role of MET kinase in cancer without the confounding effects of promiscuous protein kinase inhibition.


    Organizational Affiliation

    SGX Pharmaceuticals, San Diego, CA 92121, USA. buchanan_sean@lilly.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorA317Homo sapiensMutation(s): 4 
Gene Names: METhCG_38705tcag7.66
EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens)
Explore P08581 
Go to UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS  P08581
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SX8
Query on SX8

Download CCD File 
A
6-{[6-(1-methyl-1H-pyrazol-4-yl)[1,2,4]triazolo[4,3-b]pyridazin-3-yl]sulfanyl}quinoline
C18 H13 N7 S
BCZUAADEACICHN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SX8IC50:  4   nM  BindingDB
SX8Kd:  0.8199999928474426   nM  BindingDB
SX8Ki :  10000   nM  PDBBind
SX8IC50:  10   nM  BindingDB
SX8Kd:  3.9000000953674316   nM  BindingDB
SX8Kd:  0.1899999976158142   nM  BindingDB
SX8IC50:  3.0999999046325684   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.972α = 90
b = 46.452β = 90
c = 159.236γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2008-06-24 
  • Released Date: 2009-07-07 
  • Deposition Author(s): Hendle, J.

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2015-04-22
    Changes: Structure summary