4P5Q

Human EphA3 Kinase domain in complex with quinoxaline derivatives

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

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Ligand Structure Quality Assessment 


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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:  
    4P4C, 4P5Q, 4P5Z

  • 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 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) ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ephrin type-A receptor 3A361Homo sapiensMutation(s): 0 
Gene Names: EPHA3, ETK, ETK1, HEK, TYRO4
EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P29320 (Homo sapiens)
Explore P29320 
Go to UniProtKB:  P29320
PHAROS:  P29320
GTEx:  ENSG00000044524 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29320
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Q0B
Query on Q0B
Download Ideal Coordinates CCD File 
B [auth A]2-amino-1-(2-chlorophenyl)-N-(3-ethoxypropyl)-1H-pyrrolo[2,3-b]quinoxaline-3-carboxamide
C22 H22 Cl N5 O2
JFHMDUNXLJNQOU-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.374α = 90
b = 38.196β = 101.61
c = 75.771γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2014-03-19 
  • Released Date: 2014-08-13 
    • Deposition Author(s): Dong, J., Caflisch, A.

Revision History  (Full details and data files)

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