4P5Z

Human EphA3 Kinase domain in complex with quinoxaline derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Pyrrolo[3,2-b]quinoxaline Derivatives as Types I1/2 and II Eph Tyrosine Kinase Inhibitors: Structure-Based Design, Synthesis, and in Vivo Validation.

Unzue, A.Dong, J.Lafleur, K.Zhao, H.Frugier, E.Caflisch, A.Nevado, C.

(2014) J.Med.Chem. 57: 6834

  • DOI: 10.1021/jm5009242
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The X-ray crystal structures of the catalytic domain of the EphA3 tyrosine kinase in complex with two type I inhibitors previously discovered in silico (compounds A and B) were used to design type I1/2 and II inhibitors. Chemical synthesis of about 2 ...

    The X-ray crystal structures of the catalytic domain of the EphA3 tyrosine kinase in complex with two type I inhibitors previously discovered in silico (compounds A and B) were used to design type I1/2 and II inhibitors. Chemical synthesis of about 25 derivatives culminated in the discovery of compounds 11d (type I1/2), 7b, and 7g (both of type II), which have low-nanomolar affinity for Eph kinases in vitro and a good selectivity profile on a panel of 453 human kinases (395 nonmutant). Surface plasmon resonance measurements show a very slow unbinding rate (1/115 min) for inhibitor 7m. Slow dissociation is consistent with a type II binding mode in which the hydrophobic moiety (trifluoromethyl-benzene) of the inhibitor is deeply buried in a cavity originating from the displacement of the Phe side chain of the so-called DFG motif as observed in the crystal structure of compound 7m. The inhibitor 11d displayed good in vivo efficacy in a human breast cancer xenograft.


    Organizational Affiliation

    Department of Chemistry and ‡Department of Biochemistry, University of Zürich , Winterthurerstrasse 190, CH-8057 Zürich, 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
Q7M
Query on Q7M

Download SDF File 
Download CCD File 
A
2-amino-1-[4-({[3-(trifluoromethyl)phenyl]carbamoyl}amino)phenyl]-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide
C25 H18 F3 N7 O2
RQXYLZHJULSWPX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q7MKd: 3.9 nM (99) BINDINGDB
Q7MKd: 39.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 52.805α = 90.00
b = 38.235β = 101.46
c = 75.465γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
XSCALEdata reduction
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-03-20 
  • Released Date: 2014-08-13 
  • Deposition Author(s): Dong, J., Caflisch, A.

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release