Complex of the EphB4 kinase domain with an oxindole inhibitor
4AW5
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Transferase
    Structure Weight: 33390.61
    Molecule: EPHRIN TYPE-B RECEPTOR 4
    Polymer: 1 Type: protein Length: 291
    Chains: A
    EC#: 2.7.10.1   
    Fragment: KINASE DOMAIN, RESIDUES 605-890
    Organism: Homo sapiens
    Gene Names: HTK MYK1 TYRO11 Gene View for EPHB4
    UniProtKB: Search PDB | P54760   Protein Feature View
     
  •   Structure Validation Hide

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  •   Related Citations in PDB Entry (REMARK 1) Hide
     
  •   Source Hide
    Polymer: 1
    Scientific Name: Homo sapiens   Taxonomy   Common Name: Human Expression System: Spodoptera frugiperda  
     
  •   Related PDB Entries Hide
    Identifier Details
    2BBA   CRYSTAL STRUCTURE AND THERMODYNAMIC CHARACTERIZATION OF THEEPHB4 RECEPTOR IN COMPLEX WITH AN EPHRIN-B2 ANTAGONISTPEPTIDE REVEALS THE DETERMINANTS FOR RECEPTOR SPECIFICITY 
    2VWU   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VWV   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VWW   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VWX   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VWY   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VWZ   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VX0   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2VX1   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2X9F   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
    2XVD   EPHB4 KINASE DOMAIN INHIBITOR COMPLEX 
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    30K
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    30K C30 H31 N5 O2
    (3Z)-5-[(1-ethylpiperidin-4-yl)amino]-3-[(5- methoxy-1H-benzimidazol-2-yl)(phenyl)methylidene]- 1,3-dihydro-2H-indol-2-one
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    30K
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    30K
    N/Ain BindingDB
    IC50: 765 nM - data from BindingMOAD  
    IC50: 765 nM - data from PDBbind  
     
  •   External Domain Annotations Hide
     
  •   Structural Biology Knowledgebase Data Hide
     
 
Data in orange boxes are gathered from external resources (when available).
  Biological Assembly       
Biological assembly 1 assigned by authors and generated by PISA (software)
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  •   Deposition Summary Hide
    Authors:   Till, J.H.,  Stout, T.J.

    Deposition:   2012-05-31
    Release:   2012-08-01
     
  •   Revision History    Hide
    No revisions since initial release
     
  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.33
    R-Value: 0.194 (obs.)
    R-Free: 0.279
    Space Group: P 1 21 1
    Unit Cell:
      Length [Å] Angles [°]
    a = 46.66 α = 90.00 
    b = 53.98 β = 111.06 
    c = 63.24 γ = 90.00