ephB4 kinase domain inhibitor complex

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Inhibitors of the Tyrosine Kinase Ephb4. Part 4: Discovery and Optimization of a Benzylic Alcohol Series.

Barlaam, B.Ducray, R.Lambert-Van Der Brempt, C.Ple, P.Bardelle, C.Brooks, N.Coleman, T.Cross, D.Kettle, J.G.Read, J.

(2011) Bioorg Med Chem Lett 21: 2207

  • DOI: https://doi.org/10.1016/j.bmcl.2011.03.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Optimization of our bis-anilino-pyrimidine series of EphB4 kinase inhibitors led to the discovery of compound 12 which incorporates a key m-hydroxymethylene group on the C4 aniline. 12 displays a good kinase selectivity profile, good physical properties and pharmacokinetic parameters, suggesting it is a suitable candidate to investigate the therapeutic potential of EphB4 kinase inhibitors.

  • Organizational Affiliation

    AstraZeneca, Centre de Recherches, Z.I. la Pompelle, BP1050, 51689 Reims, Cedex 2, France.

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
PHAROS:  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
AS6 Binding MOAD:  2XVD IC50: 2 (nM) from 1 assay(s)
BindingDB:  2XVD IC50: min: 2, max: 7 (nM) from 2 assay(s)
PDBBind:  2XVD IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.708α = 90
b = 53.315β = 111.75
c = 61.33γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-06-28
    Changes: Data collection
  • Version 1.3: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description