2VX0

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 

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 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

  • DOI: 10.1016/j.bmcl.2008.04.015
  • Primary Citation of Related Structures:  2VWU, 2VWV, 2VWW
  • Also Cited By: 2VWX, 2VWY, 2VWZ, 2VX1

  • PubMed Abstract: 
  • A series of bis-anilinopyrimidines have been identified as potent inhibitors of the tyrosine kinase EphB4. Structural information from two alternative series identified from screening efforts was combined to identify the initial leads.

    A series of bis-anilinopyrimidines have been identified as potent inhibitors of the tyrosine kinase EphB4. Structural information from two alternative series identified from screening efforts was combined to identify the initial leads.


    Related Citations: 
    • 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


    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
7X7
Query on 7X7

Download SDF File 
Download CCD File 
A
N'-(5-CHLORO-1,3-BENZODIOXOL-4-YL)-N-(3-MORPHOLIN-4-YLPHENYL)PYRIMIDINE-2,4-DIAMINE
C21 H20 Cl N5 O3
PNEWIQAEGKQNCE-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 %)
7X7IC50: 580 nM (99) BINDINGDB
7X7IC50: 580 nM BINDINGMOAD
7X7IC50: 580 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 46.123α = 90.00
b = 53.492β = 110.91
c = 61.265γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling

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