4G2F

Human EphA3 kinase domain in complex with compound 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Discovery of a novel chemotype of tyrosine kinase inhibitors by fragment-based docking and molecular dynamics.

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

(2012) ACS Med Chem Lett 3: 834-838

  • DOI: 10.1021/ml3001984
  • Primary Citation of Related Structures:  
    4G2F

  • PubMed Abstract: 
  • We have discovered a novel chemical class of inhibitors of the EphB4 tyrosine kinase by fragment-based high-throughput docking followed by explicit solvent molecular dynamics simulations for assessment of the binding mode. The synthesis of a single derivative (compound 7) of the hit identified in silico has resulted in an improvement of the inhibitory potency in an enzymatic assay from 8 ...

    We have discovered a novel chemical class of inhibitors of the EphB4 tyrosine kinase by fragment-based high-throughput docking followed by explicit solvent molecular dynamics simulations for assessment of the binding mode. The synthesis of a single derivative (compound 7) of the hit identified in silico has resulted in an improvement of the inhibitory potency in an enzymatic assay from 8.4 μM to 160 nM and a ligand efficiency of 0.39 kcal/mol per non-hydrogen atom. Such remarkable improvement in affinity is due to an additional hydroxyl group involved in two favorable (buried) hydrogen bonds as predicted by molecular dynamics and validated by the crystal structure of the complex with EphA3 solved at 1.7 Å resolution.


    Organizational Affiliation

    Department of Biochemistry and Department of Organic Chemistry, University of Zurich , Winterthurerstrasse 190, CH-8057 Zurich, 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
UniProt & NIH Common Fund Data Resources
Find proteins for P29320 (Homo sapiens)
Explore P29320 
Go to UniProtKB:  P29320
PHAROS:  P29320
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C07
Query on C07

Download Ideal Coordinates CCD File 
B [auth A]1-amino-5-(5-hydroxy-2-methylphenyl)-7,8,9,10-tetrahydropyrimido[4,5-c]isoquinolin-6(5H)-one
C18 H18 N4 O2
ZQQZSFIPDUAFMC-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C07IC50 :  160   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.180 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.068α = 90
b = 38.242β = 101.59
c = 75.841γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-07-12 
  • Released Date: 2012-10-24 
  • Deposition Author(s): Dong, J., Caflisch, A.

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2014-07-16
    Changes: Database references