4TWN

Human EphA3 Kinase domain in complex with Birb796


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.706 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural Analysis of the Binding of Type I, I1/2, and II Inhibitors to Eph Tyrosine Kinases.

Dong, J.Zhao, H.Zhou, T.Spiliotopoulos, D.Rajendran, C.Li, X.D.Huang, D.Caflisch, A.

(2015) Acs Med.Chem.Lett. 6: 79-83

  • DOI: 10.1021/ml500355x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have solved the crystal structures of the EphA3 tyrosine kinase in complex with nine small-molecule inhibitors, which represent five different chemotypes and three main binding modes, i.e., types I and I1/2 (DFG in) and type II (DFG out). The thre ...

    We have solved the crystal structures of the EphA3 tyrosine kinase in complex with nine small-molecule inhibitors, which represent five different chemotypes and three main binding modes, i.e., types I and I1/2 (DFG in) and type II (DFG out). The three structures with type I1/2 inhibitors show that the higher affinity with respect to type I is due to an additional polar group (hydroxyl or pyrazole ring of indazole) which is fully buried and is involved in the same hydrogen bonds as the (urea or amide) linker of the type II inhibitors. Overall, the type I and type II binding modes belong to the lock-and-key and induced fit mechanism, respectively. In the type II binding, the scaffold in contact with the hinge region influences the position of the Phe765 side chain of the DFG motif and the orientation of the Gly-rich loop. The binding mode of Birb796 in the EphA3 kinase does not involve any hydrogen bond with the hinge region, which is different from the Birb796/p38 MAP kinase complex. Our structural analysis emphasizes the importance of accounting for structural plasticity of the ATP binding site in the design of type II inhibitors of tyrosine kinases.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ephrin type-A receptor 3
A
361Homo sapiensMutation(s): 0 
Gene 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
B96
Query on B96

Download SDF File 
Download CCD File 
A
1-(5-TERT-BUTYL-2-P-TOLYL-2H-PYRAZOL-3-YL)-3-[4-(2-MORPHOLIN-4-YL-ETHOXY)-NAPHTHALEN-1-YL]-UREA
C31 H37 N5 O3
MVCOAUNKQVWQHZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
B96Kd: 580 - 880000 nM (99) BINDINGDB
B96IC50: 1200 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.706 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.177 
  • Space Group: P 1 21 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/93 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 55.481α = 90.00
b = 38.421β = 101.50
c = 74.141γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
XSCALEdata reduction
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-07-01 
  • Released Date: 2015-05-13 
  • Deposition Author(s): Dong, J., Caflisch, A.

Revision History 

  • Version 1.0: 2015-05-13
    Type: Initial release