Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.43 kDa 
• Atom Count: 2408 
• Residue Count: 288 
• Unique protein chains: 1

5EOB

Crystal structure of CMET in complex with novel inhibitor

• DOI: 10.2210/pdb5EOB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-11-10 Released: 2016-10-19 
• Deposition Author(s): Liu, Q., Chen, T., Xu, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

Discovery of 6-(difluoro(6-(4-fluorophenyl)-[1,2,4]triazolo[4,3-b][1,2,4]triazin-3-yl)methyl)quinoline as a highly potent and selective c-Met inhibitor

Zhan, Z., Peng, X., Liu, Q., Chen, F., Ji, Y., Yao, S., Xi, Y., Lin, Y., Chen, T., Xu, Y., Ai, J., Geng, M., Duan, W.

(2016) Eur J Med Chem 116: 239-251

• PubMed: 27061987 
• DOI: 10.1016/j.ejmech.2016.03.076
• Primary Citation of Related Structures:  
  5EOB


• PubMed Abstract: 
  

c-Met/HGF overexpression has been detected in many human malignancies including tumors which are resistant to anticancer therapy. Disrupting the aberrant c-Met/HGF axis has enjoyed significant progress in both preclinical and clinical antitumor campaign. To eliminate the OCH2-related metabolic deficiency of our previously reported triazolotriazine 2, we synthesized a series of CH2-/CF2-linked triazolotriazines and assessed their c-Met activities, leading to the highly potent compound 23 with IC50 values of 0.24 nM of enzymatic activity in c-Met and 0.85 nM of cellular activity in EBC-1 cancer cell line, as well as with complete tumor regression in EBC-1 xenograft mice model at dose of 25 mg/kg via oral administration. Based on its potent anti-proliferative activities and favorable pharmacokinetic properties, 23 has been selected as a drug candidate for preclinical investigation.

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Related Citations: 

• Multisubstituted quinoxalines and pyrido[2,3-d]pyrimidines: synthesis and SAR study as tyrosine kinase c-Met inhibitors
  Wu, K., Ai, J., Liu, Q., Chen, T., Zhao, A., Peng, X., Wang, Y., Ji, Y., Yao, Q., Xu, Y., Geng, M., Zhang, A.
  (2012) Bioorg Med Chem Lett 22: 6368

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Organizational Affiliation: 

Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences (CAS), 555 Zu Chong Zhi Road, Shanghai 201203, China. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	319	Homo sapiens	Mutation(s): 0  Gene Names: MET EC: 2.7.10.1
Find proteins for P08581 (Homo sapiens) Explore P08581  Go to UniProtKB:  P08581
NIH Common Fund Data Resources
PHAROS  P08581 GTEx  ENSG00000105976

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5QQ	A	6-[bis(fluoranyl)-[6-(4-fluorophenyl)-[1,2,4]triazolo[4,3-b][1,2,4]triazin-3-yl]methyl]quinoline C20 H11 F3 N6 XQEJWZGYFBXKIF-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
5QQ	IC50:  0.23999999463558197   nM  BindingDB
5QQ	IC50:  0.8500000238418579   nM  BindingDB
5QQ	IC50:  0.46000000834465027   nM  BindingDB
5QQ	IC50:  0.23999999463558197   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.197 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.88	α = 90
b = 43.39	β = 92.68
c = 86.08	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-11-10 
• Released Date: 2016-10-19 
Deposition Author(s): Liu, Q., Chen, T., Xu, Y.

Revision History 

• Version 1.0: 2016-10-19
  Type: Initial release