3L8V

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor C-MET in complex with a biarylamine based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3L8V/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-01-04 Released: 2010-05-05 
• Deposition Author(s): Sack, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.185 

Starting Model: experimental

Literature

Design, synthesis and structure-activity relationships of novel biarylamine-based Met kinase inhibitors.

Williams, D.K., Chen, X.T., Tarby, C., Kaltenbach, R., Cai, Z.W., Tokarski, J.S., An, Y., Sack, J.S., Wautlet, B., Gullo-Brown, J., Henley, B.J., Jeyaseelan, R., Kellar, K., Manne, V., Trainor, G.L., Lombardo, L.J., Fargnoli, J., Borzilleri, R.M.

(2010) Bioorg Med Chem Lett 20: 2998-3002

• PubMed: 20382527 
• DOI: https://doi.org/10.1016/j.bmcl.2010.01.042
• Primary Citation of Related Structures:  
  3L8V


• PubMed Abstract: 
  

  Biarylamine-based inhibitors of Met kinase have been identified. Lead compounds demonstrate nanomolar potency in Met kinase biochemical assays and significant activity in the Met-driven GTL-16 human gastric carcinoma cell line. X-ray crystallography revealed that these compounds adopt a bioactive conformation, in the kinase domain, consistent with that previously seen with 2-pyridone-based Met kinase inhibitors. Compound 9b demonstrated potent in vivo antitumor activity in the GTL-16 human tumor xenograft model.

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Organizational Affiliation: 

Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA. [e-mail]

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 35.89 kDa 
• Atom Count: 2,456 
• Modelled Residue Count: 293 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	314	Homo sapiens	Mutation(s): 3  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
L8V	B [auth A]	2-({4-[(2-aminopyridin-4-yl)oxy]-3-fluorophenyl}amino)-N-(2,4-difluorophenyl)pyridine-3-carboxamide C23 H16 F3 N5 O2 VPOULRXFJKYXDN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L8V	BindingDB:  3L8V	IC50: 8 (nM) from 1 assay(s)
	PDBBind:  3L8V	IC50: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.237 
• R-Value Work: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.8	α = 90
b = 47.25	β = 90
c = 154.5	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-05 
Deposition Author(s): Sack, J.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-03-14
  Changes: Structure summary
• Version 1.3: 2021-10-13
  Changes: Database references, Derived calculations
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description