2VX1

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10.1016/j.bmcl.2008.09.087
  • Primary Citation of Related Structures:  2VWX, 2VWY, 2VWZ
  • Also Cited By: 2VX0

  • 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 a ...

    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.


    Related Citations: 
    • Inhibitors of the Tyrosine Kinase Ephb4. Part 1: Structure-Based Design and Optimization of a Series of 2,4-Bis-Anilinopyrimidines
      Bardelle, C.,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: 2776


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EPHRIN TYPE-B RECEPTOR 4
A
302Homo sapiensGene Names: EPHB4 (HTK, MYK1, TYRO11)
EC: 2.7.10.1
Find proteins for P54760 (Homo sapiens)
Go to Gene View: EPHB4
Go to UniProtKB:  P54760
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7X8
Query on 7X8

Download SDF File 
Download CCD File 
A
3-({4-[(5-CHLORO-1,3-BENZODIOXOL-4-YL)AMINO]PYRIMIDIN-2-YL}AMINO)BENZAMIDE
C18 H14 Cl N5 O3
ZVQZIVCQLFGXFZ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
7X8IC50: 220 - 900 nM (99) BINDINGDB
7X8IC50: 220 nM BINDINGMOAD
7X8IC50: 220 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.116α = 90.00
b = 53.537β = 110.90
c = 61.505γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata scaling
CrystalCleardata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection