4GG7

Crystal structure of cMET in complex with novel inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.210 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatocyte growth factor receptorA319Homo sapiensMutation(s): 0 
Gene Names: CMETMET
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08581
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0J8
Query on 0J8

Download Ideal Coordinates CCD File 
B [auth A]N-(3-nitrobenzyl)-6-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-2-(trifluoromethyl)pyrido[2,3-d]pyrimidin-4-amine
C23 H21 F3 N8 O2
OIYLUARXJZNDPY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
0J8 PDBBind:  4GG7 Ki: 6.3 (nM) from 1 assay(s)
Binding MOAD:  4GG7 IC50: 6.5 (nM) from 1 assay(s)
BindingDB:  4GG7 IC50: 6.5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.210 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.867α = 90
b = 65.867β = 90
c = 187.176γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-03
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references