Crystal structure of EphA4 kinase domain in complex with Dasatinib.

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Crystal Structure of the Epha4 Protein Tyrosine Kinase Domain in the Apo- and Dasatinib-Bound State.

Farenc, C.J.A.Hameetman, L.Zoutman, W.Tensen, C.P.Siegal, G.

(2011) FEBS Lett 585: 3593

  • DOI: https://doi.org/10.1016/j.febslet.2011.10.028
  • Primary Citation of Related Structures:  
    2Y6M, 2Y6O

  • PubMed Abstract: 

    The Eph family of receptor tyrosine kinases regulates diverse cellular processes while the over-expression of a member of this family, EphA4, has been reported in a variety of malignant carcinomas. To gain insight into molecular mechanisms and to facilitate structure-based inhibitor design, we solved the crystal structure of the native EphA4 kinase domain in both the apo and dasatinib bound forms. Analysis of the two structures provides insight into structural features of inhibitor binding and revealed a hydrophobic back-pocket in the ATP- binding site of EphA4 which was previously unidentified. The structures suggest a route towards development of novel and specific inhibitors.

  • Organizational Affiliation

    Protein Chemistry Group, Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPHRIN TYPE-A RECEPTOR 4291Mus musculusMutation(s): 0 
Find proteins for Q03137 (Mus musculus)
Explore Q03137 
Go to UniProtKB:  Q03137
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03137
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 1N1

Download Ideal Coordinates CCD File 
C22 H26 Cl N7 O2 S
Binding Affinity Annotations 
IDSourceBinding Affinity
1N1 BindingDB:  2Y6O Kd: min: 0.09, max: 1.2 (nM) from 4 assay(s)
Binding MOAD:  2Y6O IC50: 25 (nM) from 1 assay(s)
PDBBind:  2Y6O IC50: 25 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.412α = 90
b = 91.636β = 90
c = 98.346γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-09
    Changes: Database references
  • Version 1.2: 2012-01-11
    Changes: Other
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description