3F66

Human c-Met Kinase in complex with quinoxaline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3F66/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2008-11-05 Released: 2008-12-23 
• Deposition Author(s): Meier, C., Ceska, T.

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Experimental Data Snapshot

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

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

• PubMed: 19059779 
• 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.

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Organizational Affiliation: 

UCB Celltech, 216 Bath Road, Slough SL1 3WE, United Kingdom. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 68.92 kDa 
• Atom Count: 5,160 
• Modelled Residue Count: 557 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A, B	298	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IHX	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	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	GAMMA-BUTYROLACTONE C4 H6 O2 YEJRWHAVMIAJKC-UHFFFAOYSA-N
NA	J [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
IHX	BindingDB:  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 = 47.377	α = 100.7
b = 47.587	β = 103.62
c = 75.6	γ = 98.29

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-12-23 
Deposition Author(s): Meier, C., Ceska, T.

Revision History  

• 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