4L09

Crystal structure of human tankyrase 2 in complex with 4-(4-oxo-4H-chromen-2-yl)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of tankyrase inhibiting flavones with increased potency and isoenzyme selectivity.

Narwal, M.Koivunen, J.Haikarainen, T.Obaji, E.Legala, O.E.Venkannagari, H.Joensuu, P.Pihlajaniemi, T.Lehtio, L.

(2013) J.Med.Chem. 56: 7880-7889

  • DOI: 10.1021/jm401463y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tankyrases are ADP-ribosyltransferases that play key roles in various cellular pathways, including the regulation of cell proliferation, and thus, they are promising drug targets for the treatment of cancer. Flavones have been shown to inhibit tankyr ...

    Tankyrases are ADP-ribosyltransferases that play key roles in various cellular pathways, including the regulation of cell proliferation, and thus, they are promising drug targets for the treatment of cancer. Flavones have been shown to inhibit tankyrases and we report here the discovery of more potent and selective flavone derivatives. Commercially available flavones with single substitutions were used for structure-activity relationship studies, and cocrystal structures of the 18 hit compounds were analyzed to explain their potency and selectivity. The most potent inhibitors were also tested in a cell-based assay, which demonstrated that they effectively antagonize Wnt signaling. To assess selectivity, they were further tested against a panel of homologous human ADP-ribosyltransferases. The most effective compound, 22 (MN-64), showed 6 nM potency against tankyrase 1, isoenzyme selectivity, and Wnt signaling inhibition. This work forms a basis for rational development of flavones as tankyrase inhibitors and guides the development of other structurally related inhibitors.


    Organizational Affiliation

    Department of Biochemistry and Biocenter Oulu, University of Oulu , Oulu 90570, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tankyrase-2
A, B
191Homo sapiensMutation(s): 0 
Gene Names: TNKS2 (PARP5B, TANK2, TNKL)
EC: 2.4.2.30
Find proteins for Q9H2K2 (Homo sapiens)
Go to Gene View: TNKS2
Go to UniProtKB:  Q9H2K2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tankyrase-2
C, D
49Homo sapiensMutation(s): 0 
Gene Names: TNKS2 (PARP5B, TANK2, TNKL)
EC: 2.4.2.30
Find proteins for Q9H2K2 (Homo sapiens)
Go to Gene View: TNKS2
Go to UniProtKB:  Q9H2K2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
1UR
Query on 1UR

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Download CCD File 
A, B
4-(4-oxo-4H-chromen-2-yl)benzoic acid
C16 H10 O4
GDILHIUGUNCNDU-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1URIC50: 850 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.164 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 91.650α = 90.00
b = 98.440β = 90.00
c = 118.210γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
XDSdata reduction
REFMACrefinement
GDAdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-30
    Type: Initial release
  • Version 1.1: 2014-01-15
    Type: Database references