4DEG | pdb_00004deg

Crystal structure of c-Met in complex with triazolopyridazine inhibitor 2

• PDB DOI: https://doi.org/10.2210/pdb4DEG/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2012-01-20 Released: 2012-05-30 
• Deposition Author(s): Whittington, D.A., Bellon, S.F., Long, A.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Discovery and optimization of a potent and selective triazolopyridinone series of c-Met inhibitors.

Bode, C.M., Boezio, A.A., Albrecht, B.K., Bellon, S.F., Berry, L., Broome, M.A., Choquette, D., Dussault, I., Lewis, R.T., Lin, M.H., Rex, K., Whittington, D.A., Yang, Y., Harmange, J.C.

(2012) Bioorg Med Chem Lett 22: 4089-4093

• PubMed: 22595176 
• DOI: https://doi.org/10.1016/j.bmcl.2012.04.072
• Primary Citation of Related Structures:  
  4DEG, 4DEH, 4DEI


• PubMed Abstract: 
  

  Deregulation of the receptor tyrosine kinase c-Met has been implicated in several human cancers and is an attractive target for small molecule drug discovery. Herein, we report the discovery of a structurally diverse series of carbon-linked quinoline triazolopyridinones, which demonstrates nanomolar inhibition of c-Met kinase activity. This novel series of inhibitors exhibits favorable pharmacokinetics as well as potent inhibition of HGF-mediated c-Met phosphorylation in a mouse liver pharmacodynamic model.

---

Organizational Affiliation: 

Amgen Inc., 360 Binney St., Cambridge, MA 02142, 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: 35.62 kDa 
• Atom Count: 2,523 
• Modelled Residue Count: 286 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	309	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0JJ	B [auth A]	7-methoxy-N-{[6-(3-methyl-1,2-thiazol-5-yl)[1,2,4]triazolo[4,3-b]pyridazin-3-yl]methyl}-1,5-naphthyridin-4-amine C19 H16 N8 O S QMWKLCXWSJTEFT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0JJ	BindingDB:  4DEG	Ki: 3.2 (nM) from 1 assay(s)
		IC50: min: 3, max: 6 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.042	α = 90
b = 43.012	β = 90
c = 157.954	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Whittington, D.A., Bellon, S.F., Long, A.M.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-06-20
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations