Experimental Data Snapshot

  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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Ligand Structure Quality Assessment 

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Discovery, optimization and biological evaluation for novel c-Met kinase inhibitors

Yuan, H.Liu, Q.Zhang, L.Hu, S.Chen, T.Li, H.Chen, Y.Xu, Y.Lu, T.

(2018) Eur J Med Chem 143: 491-502

  • DOI: https://doi.org/10.1016/j.ejmech.2017.11.073
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The c-Met kinase has emerged as an attractive target for developing antitumor agents because of its close relationship with the development of many human cancers, poor clinical outcomes and even drug resistance. A series of novel c-Met kinase inhibitors have been identified with multiple workflow in this work, including virtual screening, X-ray crystallography, biological evaluation and structural optimization. The experimentally determined crystal structure of the best hit compound HL-11 in c-Met kinase domain was highly consistent with the computational prediction. Comparison of the hit compounds with different c-Met kinase inhibitory activity by molecular dynamics simulations suggested the key protein-ligand interactions for structural optimization. Based on these, structural optimization produced compound 11e with better c-Met kinase inhibitory activity and improved anti-proliferative activity. These experimental findings proved the reliability and efficiency of our in silico methods. This strategy will facilitate further lead discovery and optimization for novel c-Met kinase inhibitors.

  • Organizational Affiliation

    Laboratory of Molecular Design and Drug Discovery, School of Science, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China; State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, Institute of Pharmaceutical Research, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hepatocyte growth factor receptor319Homo sapiensMutation(s): 0 
Gene Names: MET
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6TD (Subject of Investigation/LOI)
Query on 6TD

Download Ideal Coordinates CCD File 
B [auth A]2-[3-(4-methoxybenzyl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazol-6-yl]-1H-indole
C19 H15 N5 O S
Binding Affinity Annotations 
IDSourceBinding Affinity
6TD BindingDB:  5YA5 IC50: min: 79, max: 190 (nM) from 2 assay(s)
Binding MOAD:  5YA5 IC50: 190 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.89 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.36α = 90
b = 47.34β = 90
c = 158.69γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2018-07-04 
  • Deposition Author(s): Liu, Q., Xu, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description