2VWX

ephB4 kinase domain inhibitor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 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, 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
EPHRIN TYPE-B RECEPTOR 4A302Homo sapiensMutation(s): 1 
Gene Names: EPHB4HTKMYK1TYRO11
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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP54760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7X4
Query on 7X4

Download Ideal Coordinates CCD File 
B [auth A]3-({4-[(5-chloro-1,3-benzodioxol-4-yl)amino]pyrimidin-2-yl}amino)benzenesulfonamide
C17 H14 Cl N5 O4 S
TZHCXOMEOHEZDX-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7X4 Binding MOAD:  2VWX IC50: 40 (nM) from 1 assay(s)
BindingDB:  2VWX IC50: min: 40, max: 172 (nM) from 2 assay(s)
PDBBind:  2VWX IC50: 40 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.777α = 90
b = 53.451β = 110.57
c = 61.347γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata 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: 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