2XYU

Crystal structure of EphA4 kinase domain in complex with VUF 12058


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.117 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Fragment Based Lead Discovery of Small Molecule Inhibitors for the Epha4 Receptor Tyrosine Kinase.

Van Linden, O.P.Farenc, C.J.A.Zoutman, W.H.Hameetman, L.Wijtmans, M.Leurs, R.Tensen, C.P.Siegal, G.De Esch, I.J.

(2012) Eur.J.Med.Chem. 47: 493

  • DOI: 10.1016/j.ejmech.2011.11.020

  • PubMed Abstract: 
  • The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commerc ...

    The in silico identification, optimization and crystallographic characterization of a 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine scaffold as an inhibitor for the EPHA4 receptor tyrosine kinase is described. A database containing commercially available compounds was subjected to an in silico screening procedure which was focused on finding novel, EPHA4 hinge binding fragments. This resulted in the identification of 6,7,8,9-tetrahydro-3H-pyrazolo[3,4-c]isoquinolin-1-amine derivatives as EPHA4 inhibitors. Hit exploration yielded a compound with 2 μM (IC(50)) affinity for the EPHA4 receptor tyrosine kinase domain. Soaking experiments into a crystal of the EPHA4 kinase domain gave a 2.11Å X-ray structure of the EPHA4 - inhibitor complex, which confirmed the binding mode of the scaffold as proposed by the initial in silico work. The results underscore the strength of fragment based in silico screening as a tool for the discovery of novel lead compounds as small molecule kinase inhibitors.


    Organizational Affiliation

    Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-A RECEPTOR 4,
A
285Mus musculusMutation(s): 0 
Gene Names: Epha4 (Sek, Sek1)
EC: 2.7.10.1
Find proteins for Q03137 (Mus musculus)
Go to UniProtKB:  Q03137
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Q9G
Query on Q9G

Download SDF File 
Download CCD File 
A
5-(5-FLUORO-2-METHYLPHENYL)-6,7,8,9-TETRAHYDRO-3H-PYRAZOLO[3,4-C]ISOQUINOLIN-1-AMINE
C17 H17 F N4
YPULTKAHHAYKOE-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q9GIC50: 4500 nM (99) BINDINGDB
Q9GIC50: 4500 nM BINDINGMOAD
Q9GIC50: 4500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.117 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.544α = 90.00
b = 91.545β = 90.00
c = 97.959γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
AMoREphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-28
    Type: Other
  • Version 1.2: 2012-01-25
    Type: Other
  • Version 1.3: 2012-02-01
    Type: Other