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Crystal Structure of TNF-alpha with a small molecule inhibitor
2AZ5
Primary Citation
 
 
  •   Molecular Description Hide
    Classification: Cytokine
    Structure Weight: 66738.44
    Molecule: Tumor necrosis factor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF-a) (Cachectin) [Contains: Tumor necrosis factor, membrane form; Tumor necrosis factor, soluble form]
    Polymer: 1 Type: protein Length: 148
    Chains: A, B, C, D
    Organism Homo sapiens
    Gene Names TNF TNFA TNFSF2
    UniProtKB:   Protein Feature View | Search PDB | P01375  
     
  •   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: Escherichia coli bl21(de3)  
     
  •   Ligand Chemical Component Hide
    Identifier Formula Name View Interactions
    307
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    307 C32 H32 F3 N3 O2
    6,7-DIMETHYL-3-[(METHYL{2-[METHYL({1-[3-(TRIFLUOROMETHYL)PHENYL]- 1H-INDOL-3-YL}METHYL)AMINO]ETHYL}AMINO)METHYL]- 4H-CHROMEN-4-ONE
     
  •   External Ligand Annotations Hide
    Identifier   Binding Affinity (Sequence Identity %)
    307
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    307
    Kd: 5360 - 13000 nM (100) - data from BindingDB  
    IC50: 22000 nM - data from BindingMOAD  
    N/Ain 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
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  •   Deposition Summary Hide
    Authors:   He, M.M.

    Deposition:   2005-09-09
    Release:   2005-11-29
    Last Modified (REVDAT):   2009-02-24
     
  •   Revision History    Hide
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    2011-07-13
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  •   Experimental Details Hide
    Method:   X-RAY DIFFRACTION
    Exp. Data:
      Structure Factors
    EDS  
    Resolution[Å]:   2.10
    R-Value: 0.227 (obs.)
    R-Free: 0.278
    Space Group: H 3
    Unit Cell:
      Length [Å] Angles [°]
    a = 165.25 α = 90.00 
    b = 165.25 β = 90.00 
    c = 63.73 γ = 120.00