2Y6O

Crystal structure of EphA4 kinase domain in complex with Dasatinib.

• PDB DOI: https://doi.org/10.2210/pdb2Y6O/pdb

• Classification: TRANSFERASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-25 Released: 2011-11-02 
• Deposition Author(s): Farenc, C.J.A., Celie, P.H.N., Siegal, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.201 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Starting Model: experimental

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

• PubMed: 22036717 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.42 kDa 
• Atom Count: 2,559 
• Modelled Residue Count: 263 
• Deposited Residue Count: 291 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EPHRIN TYPE-A RECEPTOR 4	A	291	Mus musculus	Mutation(s): 0  EC: 2.7.10.1
UniProt
Find proteins for Q03137 (Mus musculus) Explore Q03137  Go to UniProtKB:  Q03137

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1N1	B [auth A]	N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE C22 H26 Cl N7 O2 S ZBNZXTGUTAYRHI-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1N1	BindingDB:  2Y6O	Kd: min: 0.09, max: 1.2 (nM) from 4 assay(s)
	PDBBind:  2Y6O	IC50: 25 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 32.412	α = 90
b = 91.636	β = 90
c = 98.346	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Farenc, C.J.A., Celie, P.H.N., Siegal, G.

Revision History  

• 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