2Y6O

Crystal structure of EphA4 kinase domain in complex with Dasatinib.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.543 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1016/j.febslet.2011.10.028
  • Primary Citation of Related Structures:  

  • 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 fac ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-A RECEPTOR 4
A
291Mus 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1N1
Query on 1N1

Download SDF File 
Download CCD File 
A
N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE
Dasatinib
C22 H26 Cl N7 O2 S
ZBNZXTGUTAYRHI-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1N1Kd: 0.1 - 1.2 nM (85) BINDINGDB
1N1IC50: 25 nM BINDINGMOAD
1N1IC50: 25 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.543 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.180 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 32.412α = 90.00
b = 91.636β = 90.00
c = 98.346γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
AMoREphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2011-11-09
    Type: Database references
  • Version 1.2: 2012-01-11
    Type: Other