4GG5

Crystal structure of CMET in complex with novel inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4GG5/pdb

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


• Deposited: 2012-08-05 Released: 2012-10-03 
• Deposition Author(s): Liu, Q.F., Chen, T.T., Xu, Y.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.268 
• R-Value Work: 0.210 
• R-Value Observed: 0.216 

Literature

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: 6368-6372

• PubMed: 22985853 
• DOI: https://doi.org/10.1016/j.bmcl.2012.08.075
• Primary Citation of Related Structures:  
  4GG5, 4GG7


• PubMed Abstract: 
  

  Two series of new analogues were designed by replacing the quinoline scaffold of our earlier lead 2 (zgw-atinib) with quinoxaline and pyrido[2,3-d]pyrimidine frameworks. Moderate c-Met inhibitory activity was observed in the quinoxaline series. Among the pyrido[2,3-d]pyrimidine series, compounds 13a-c possessing an O-linkage were inactive, whilst the N-linked analogues 15a-c retained c-Met inhibitory potency. Highest activity was observed in the 3-nitrobenzyl analog 15b that showed an IC(50) value of 6.5 nM. Further structural modifications based on this compound were undergoing.

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Organizational Affiliation: 

Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.

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: 36.48 kDa 
• Atom Count: 2,265 
• Modelled Residue Count: 274 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatocyte growth factor receptor	A	319	Homo sapiens	Mutation(s): 0  Gene Names: c-MET, 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
0J3	B [auth A]	3-(4-methylpiperazin-1-yl)-N-(3-nitrobenzyl)-7-(trifluoromethyl)quinolin-5-amine C22 H22 F3 N5 O2 JIYPGFPFAVEPFX-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0J3	PDBBind:  4GG5	IC50: 0.93 (nM) from 1 assay(s)
	BindingDB:  4GG5	IC50: 0.93 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.42 Å
• R-Value Free: 0.268 
• R-Value Work: 0.210 
• R-Value Observed: 0.216 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.641	α = 90
b = 65.641	β = 90
c = 186.174	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-03 
Deposition Author(s): Liu, Q.F., Chen, T.T., Xu, Y.C.

Revision History  

• Version 1.0: 2012-10-03
  Type: Initial release
  
• Version 1.1: 2012-10-17
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations