4P4C

Human EphA3 Kinase domain in complex with quinoxaline derivatives


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 6834-6844

  • DOI: 10.1021/jm5009242
  • Primary Citation of Related Structures:  
    4P5Z, 4P4C, 4P5Q

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPH receptor A3A361Homo sapiensMutation(s): 0 
Gene Names: EPHA3ETKETK1HEKTYRO4
EC: 2.7.10.1
Find proteins for P29320 (Homo sapiens)
Explore P29320 
Go to UniProtKB:  P29320
NIH Common Fund Data Resources
PHAROS  P29320
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
25Q
Query on 25Q

Download Ideal Coordinates CCD File 
A
2-amino-1-(3-methoxyphenyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide
C18 H15 N5 O2
CHHKMVNVTYIPGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.914α = 90
b = 38.164β = 101.59
c = 75.527γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
XDSdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-03-12 
  • Released Date: 2014-08-13 
  • Deposition Author(s): Dong, J., Caflisch, A.

Funding OrganizationLocationGrant Number
KrebsligaSwitzerland--
Swiss National Science FoundationSwitzerland--

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Database references, Derived calculations, Other, Refinement description, Source and taxonomy