3LQ8

Structure of the kinase domain of c-Met bound to XL880 (GSK1363089)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Inhibition of tumor cell growth, invasion, and metastasis by EXEL-2880 (XL880, GSK1363089), a novel inhibitor of HGF and VEGF receptor tyrosine kinases.

Qian, F., Engst, S., Yamaguchi, K., Yu, P., Won, K.A., Mock, L., Lou, T., Tan, J., Li, C., Tam, D., Lougheed, J., Yakes, F.M., Bentzien, F., Xu, W., Zaks, T., Wooster, R., Greshock, J., Joly, A.H.

(2009) Cancer Res 69: 8009-8016

  • DOI: 10.1158/0008-5472.CAN-08-4889
  • Primary Citation of Related Structures:  
    3LQ8

  • PubMed Abstract: 

    • The Met receptor tyrosine kinase and its ligand, hepatocyte growth factor (HGF), are overexpressed and/or activated in a wide variety of human malignancies. Vascular endothelial growth factor (VEGF) receptors are expressed on the surface of vascular endothelial cells and cooperate with Met to induce tumor invasion and vascularization ...

    The Met receptor tyrosine kinase and its ligand, hepatocyte growth factor (HGF), are overexpressed and/or activated in a wide variety of human malignancies. Vascular endothelial growth factor (VEGF) receptors are expressed on the surface of vascular endothelial cells and cooperate with Met to induce tumor invasion and vascularization. EXEL-2880 (XL880, GSK1363089) is a small-molecule kinase inhibitor that targets members of the HGF and VEGF receptor tyrosine kinase families, with additional inhibitory activity toward KIT, Flt-3, platelet-derived growth factor receptor beta, and Tie-2. Binding of EXEL-2880 to Met and VEGF receptor 2 (KDR) is characterized by a very slow off-rate, consistent with X-ray crystallographic data showing that the inhibitor is deeply bound in the Met kinase active site cleft. EXEL-2880 inhibits cellular HGF-induced Met phosphorylation and VEGF-induced extracellular signal-regulated kinase phosphorylation and prevents both HGF-induced responses of tumor cells and HGF/VEGF-induced responses of endothelial cells. In addition, EXEL-2880 prevents anchorage-independent proliferation of tumor cells under both normoxic and hypoxic conditions. In vivo, these effects produce significant dose-dependent inhibition of tumor burden in an experimental model of lung metastasis. Collectively, these data indicate that EXEL-2880 may prevent tumor growth through a direct effect on tumor cell proliferation and by inhibition of invasion and angiogenesis mediated by HGF and VEGF receptors.

    Organizational Affiliation: 

    Exelixis, Inc, South San Francisco, California 94083, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorA302Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
88Z
Query on 88Z
Download Ideal Coordinates CCD File 
 B [auth A]N-(3-fluoro-4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy)quinolin-4-yl]oxy}phenyl)-N'-(4-fluorophenyl)cyclopropane-1,1-dicarboxamide
C34 H34 F2 N4 O6
CXQHYVUVSFXTMY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
88ZIC50:  1.5   nM  BindingDB
88ZIC50:  9.199999809265137   nM  BindingDB
88ZIC50:  0.4000000059604645   nM  BindingDB
88ZIC50:  1.600000023841858   nM  BindingDB
88ZIC50:  1.899999976158142   nM  BindingDB
88ZIC50:  19   nM  BindingDB
88ZIC50:  1.7999999523162842   nM  BindingDB
88ZIC50:  1.2000000476837158   nM  BindingDB
88ZIC50:  4   nM  BindingDB
88ZIC50:  1.8899999856948853   nM  BindingDB
88ZIC50:  2.0999999046325684   nM  BindingDB
88ZIC50:  1.100000023841858   nM  BindingDB
88ZIC50:  14   nM  BindingDB
88ZIC50:  3.200000047683716   nM  BindingDB
88ZIC50 :  0.4000000059604645   nM  PDBBind
88ZIC50:  0.5   nM  BindingDB
88ZIC50:  0.4000000059604645   nM  Binding MOAD
88ZIC50:  7.900000095367432   nM  BindingDB
88ZIC50:  1.399999976158142   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.925α = 90
b = 43.017β = 91.61
c = 89.618γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance