3CTH | pdb_00003cth

Crystal structure of the tyrosine kinase domain of the hepatocyte growth factor receptor c-met in complex with a aminopyridine based inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3CTH/pdb

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


• Deposited: 2008-04-14 Released: 2008-06-10 
• Deposition Author(s): Sack, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.273 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Discovery of orally active pyrrolopyridine- and aminopyridine-based Met kinase inhibitors

Cai, Z.-W., Wei, D., Schroeder, G.M., Cornelius, L.A., Kim, K., Chen, X.-T., Schmidt, R.J., Williams, D.K., Tokarski, J.S., An, Y., Sack, J.S., Manne, V., Kamath, A., Zhang, Y., Marathe, P., Hunt, J.T., Lombardo, L.J., Fargnoli, J., Borzilleri, R.M.

(2008) Bioorg Med Chem Lett 18: 3224-3229

• PubMed: 18479916 
• DOI: https://doi.org/10.1016/j.bmcl.2008.04.047
• Primary Citation Related Structures: 
  3CTH, 3CTJ


• PubMed Abstract: 
  

  A series of acylurea analogs derived from pyrrolopyridine and aminopyridine scaffolds were identified as potent inhibitors of Met kinase activity. The SAR at various positions of the two kinase scaffolds was investigated. These studies led to the discovery of compounds 3b and 20b, which demonstrated favorable pharmacokinetic properties in mice and significant antitumor activity in a human gastric carcinoma 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: 35.83 kDa 
• Atom Count: 2,461 
• Modeled Residue Count: 295 
• 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
319	B [auth A]	N-({4-[(2-aminopyridin-4-yl)oxy]-3-fluorophenyl}carbamoyl)-2-(4-fluorophenyl)acetamide C20 H16 F2 N4 O3 USBSTVPJNQLYEM-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
319	BindingDB:  3CTH	IC50: 35 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.273 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.752	α = 90
b = 47.637	β = 90
c = 152.471	γ = 90

Software Package:

Software Name	Purpose
BUSTER-TNT	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-10 
Deposition Author(s): Sack, J.

Revision History  

• Version 1.0: 2008-06-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection