3CD8

X-ray Structure of c-Met with triazolopyridazine Inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb3CD8/pdb

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


• Deposited: 2008-02-26 Released: 2008-04-29 
• Deposition Author(s): Bellon, S.F., Albrecht, B.K., Harmange, J.-C., Bauer, D., Choquette, D., Dussault, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Discovery and Optimization of Triazolopyridazines as Potent and Selective Inhibitors of the c-Met Kinase.

Albrecht, B.K., Harmange, J.C., Bauer, D., Berry, L., Bode, C., Boezio, A.A., Chen, A., Choquette, D., Dussault, I., Fridrich, C., Hirai, S., Hoffman, D., Larrow, J.F., Kaplan-Lefko, P., Lin, J., Lohman, J., Long, A.M., Moriguchi, J., O'Connor, A., Potashman, M.H., Reese, M., Rex, K., Siegmund, A., Shah, K., Shimanovich, R., Springer, S.K., Teffera, Y., Yang, Y., Zhang, Y., Bellon, S.F.

(2008) J Med Chem 51: 2879-2882

• PubMed: 18426196 
• DOI: https://doi.org/10.1021/jm800043g
• Primary Citation of Related Structures:  
  3CCN, 3CD8


• PubMed Abstract: 
  

  Tumorigenesis is a multistep process in which oncogenes play a key role in tumor formation, growth, and maintenance. MET was discovered as an oncogene that is activated by its ligand, hepatocyte growth factor. Deregulated signaling in the c-Met pathway has been observed in multiple tumor types. Herein we report the discovery of potent and selective triazolopyridazine small molecules that inhibit c-Met activity.

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Organizational Affiliation: 

Amgen Inc., Cambridge, MA 02139, 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: 35.73 kDa 
• Atom Count: 2,357 
• Modelled Residue Count: 278 
• Deposited Residue Count: 310 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	310	Homo sapiens	Mutation(s): 1  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
L5G	B [auth A]	7-methoxy-4-[(6-phenyl[1,2,4]triazolo[4,3-b]pyridazin-3-yl)methoxy]quinoline C22 H17 N5 O2 HEAIZQNMNCHNFD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
L5G	PDBBind:  3CD8	IC50: 9 (nM) from 1 assay(s)
	BindingDB:  3CD8	IC50: min: 9, max: 90 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.287 
• R-Value Work: 0.233 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.008	α = 90
b = 43.208	β = 90
c = 158.219	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-29 
Deposition Author(s): Bellon, S.F., Albrecht, B.K., Harmange, J.-C., Bauer, D., Choquette, D., Dussault, I.

Revision History  

• Version 1.0: 2008-04-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description