2X9F

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

Inhibitors of the Tyrosine Kinase Ephb4. Part 3: Identification of Non-Benzodioxole-Based Kinase Inhibitors.

Bardelle, C.Barlaam, B.Brooks, N.Coleman, T.Cross, D.Ducray, R.Green, I.Brempt, C.L.Olivier, A.Read, J.

(2010) Bioorg Med Chem Lett 20: 6242

  • DOI: https://doi.org/10.1016/j.bmcl.2010.08.100
  • Primary Citation of Related Structures:  
    2X9F

  • PubMed Abstract: 

    Starting from the initial bis-anilinopyrimidine 1, good potency against EphB4 was retained when benzodioxole at C-4 was replaced by an indazole. The key interactions of the indazole with the protein were characterised by crystallographic studies. Further optimisation led to compound 20, a potent inhibitor of the EphB4 and Src kinases with good pharmacokinetics in various preclinical species and high fraction unbound in plasma. Compound 20 may be used as a tool for evaluating the potential of EphB4 kinase inhibitors in vivo.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EPHRIN TYPE-B RECEPTOR 4302Homo sapiensMutation(s): 1 
EC: 2.7.10.1
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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
X9F BindingDB:  2X9F IC50: min: 61, max: 2530 (nM) from 2 assay(s)
PDBBind:  2X9F IC50: 61 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.12α = 90
b = 52.479β = 112.05
c = 61.369γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-29
    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: 2018-04-04
    Changes: Data collection
  • Version 1.4: 2019-04-03
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2019-04-24
    Changes: Data collection, Source and taxonomy
  • Version 1.6: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.7: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description