4GK2

Human EphA3 Kinase domain in complex with ligand 66


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.195 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Optimization of Inhibitors of the Tyrosine Kinase EphB4. 2. Cellular Potency Improvement and Binding Mode Validation by X-ray Crystallography.

Lafleur, K.Dong, J.Huang, D.Caflisch, A.Nevado, C.

(2013) J.Med.Chem. 56: 84-96

  • DOI: 10.1021/jm301187e
  • Primary Citation of Related Structures:  4GK3, 4GK4

  • PubMed Abstract: 
  • Inhibition of the tyrosine kinase erythropoietin-producing human hepatocellular carcinoma receptor B4 (EphB4) is an effective strategy for the treatment of solid tumors. We have previously reported a low nanomolar ATP-competitive inhibitor of EphB4 d ...

    Inhibition of the tyrosine kinase erythropoietin-producing human hepatocellular carcinoma receptor B4 (EphB4) is an effective strategy for the treatment of solid tumors. We have previously reported a low nanomolar ATP-competitive inhibitor of EphB4 discovered in silico by fragment-based high-throughput docking combined with explicit solvent molecular dynamics simulations. Here we present a second generation of EphB4 inhibitors that show high inhibitory potency in both enzymatic and cell-based assays while preserving the appealing selectivity profile exhibited by the parent compound. In addition, respectable levels of antiproliferative activity for these compounds have been obtained. Finally, the binding mode predicted by docking and molecular dynamics simulations is validated by solving the crystal structures of three members of this chemical class in complex with the EphA3 tyrosine kinase whose ATP-binding site is essentially identical to that of EphB4.


    Organizational Affiliation

    Department of Organic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPH receptor A3
A
361Homo sapiensGene Names: EPHA3 (ETK, ETK1, HEK, TYRO4)
EC: 2.7.10.1
Find proteins for P29320 (Homo sapiens)
Go to Gene View: EPHA3
Go to UniProtKB:  P29320
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L66
Query on L66

Download SDF File 
Download CCD File 
A
7-(5-hydroxy-2-methylphenyl)-8-(2-methoxyphenyl)-1-methyl-1H-imidazo[2,1-f]purine-2,4(3H,8H)-dione
C22 H19 N5 O4
JTWMOWRMSZZHDR-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
L66IC50: 40 nM (99) BINDINGDB
L66IC50: 1.6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.195 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.601α = 90.00
b = 38.195β = 101.71
c = 75.704γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
XDSdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-10 
  • Released Date: 2013-01-23 
  • Deposition Author(s): Dong, J., Caflisch, A.

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release