ephB4 kinase domain inhibitor complex

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.6 of the entry. See complete history


Inhibitors of the Tyrosine Kinase Ephb4. Part 2: Structure-Based Discovery and Optimisation of 3,5-Bis Substituted Anilinopyrimidines.

Bardelle, C.Coleman, T.Cross, D.Davenport, S.Kettle, J.G.Ko, E.J.Leach, A.G.Mortlock, A.Read, J.Roberts, N.J.Robins, P.Williams, E.J.

(2008) Bioorg Med Chem Lett 18: 5717

  • DOI: https://doi.org/10.1016/j.bmcl.2008.09.087
  • Primary Citation of Related Structures:  
    2VWX, 2VWY, 2VWZ, 2VX1

  • PubMed Abstract: 

    Crystallographic studies of a range of 3-substituted anilinopyrimidine inhibitors of EphB4 have highlighted two alternative C-2 aniline conformations and this discovery has been exploited in the design of a highly potent series of 3,5-disubstituted anilinopyrimidines. The observed range of cellular activities has been rationalised on the basis of physicochemical and structural characteristics.

  • Organizational Affiliation

    AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire SK10 4TG, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPHRIN TYPE-B RECEPTOR 4302Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P54760 (Homo sapiens)
Explore P54760 
Go to UniProtKB:  P54760
GTEx:  ENSG00000196411 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54760
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
7X6 BindingDB:  2VWZ IC50: min: 741, max: 794 (nM) from 2 assay(s)
PDBBind:  2VWZ IC50: 794 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.81α = 90
b = 53.567β = 110.64
c = 61.373γ = 90
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-06-28
    Changes: Data collection
  • Version 1.4: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description