3F66

Human c-Met Kinase in complex with quinoxaline inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.168 

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This is version 1.2 of the entry. See complete history. 


Literature

Discovery of a novel series of quinoxalines as inhibitors of c-Met kinase.

Porter, J., Lumb, S., Lecomte, F., Reuberson, J., Foley, A., Calmiano, M., le Riche, K., Edwards, H., Delgado, J., Franklin, R.J., Gascon-Simorte, J.M., Maloney, A., Meier, C., Batchelor, M.

(2009) Bioorg Med Chem Lett 19: 397-400

  • DOI: https://doi.org/10.1016/j.bmcl.2008.11.062
  • Primary Citation of Related Structures:  
    3F66

  • PubMed Abstract: 

    A series of quinoxaline inhibitors of c-Met kinase is described. The postulated binding mode was confirmed by an X-ray crystal structure and optimisation of the series was performed on the basis of this structure. Future directions for development of the series are discussed together with the identification of a novel quinoline scaffold.

    • Organizational Affiliation: 

    UCB Celltech, 216 Bath Road, Slough SL1 3WE, United Kingdom. john.porter@ucb-group.com


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor
A, B
298Homo sapiensMutation(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
GTEx:  ENSG00000105976 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IHX
Query on IHX
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		3-[3-(4-methylpiperazin-1-yl)-7-(trifluoromethyl)quinoxalin-5-yl]phenol
C20 H19 F3 N4 O
QNCYYRHIUFGGJX-UHFFFAOYSA-N
GBL
Query on GBL
Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B]		GAMMA-BUTYROLACTONE
C4 H6 O2
YEJRWHAVMIAJKC-UHFFFAOYSA-N
NA
Query on NA
Download Ideal Coordinates CCD File 
J [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
IHX BindingDB:  3F66 IC50: 900 (nM) from 1 assay(s)
Binding MOAD:  3F66 IC50: 900 (nM) from 1 assay(s)
PDBBind:  3F66 IC50: 900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.168 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.377α = 100.7
b = 47.587β = 103.62
c = 75.6γ = 98.29
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations