4HLM

Crystal structure of Tankyrase 2 in complex with 3',4'-Dihydroxyflavone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Screening and structural analysis of flavones inhibiting tankyrases.

Narwal, M.Haikarainen, T.Fallarero, A.Vuorela, P.M.Lehtio, L.

(2013) J.Med.Chem. 56: 3507-3517

  • DOI: 10.1021/jm3018783
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavonoids are known for their beneficial effects on human health, and therefore the therapeutic potential of these compounds have been extensively studied. Flavone has been previously identified as a tankyrase inhibitor, and to further elucidate whe ...

    Flavonoids are known for their beneficial effects on human health, and therefore the therapeutic potential of these compounds have been extensively studied. Flavone has been previously identified as a tankyrase inhibitor, and to further elucidate whether tankyrases would be inhibited by other flavonoids, we performed a systematic screening of tankyrase 2 inhibitory activity using 500 natural and naturally derived flavonoids covering nine different flavonoid classes. All identified tankyrase inhibitors were flavones. We report crystal structures of all the hit compounds in complex with the catalytic domain of human tankyrase 2. Flavone derivatives in all 10 crystal structures bind to the nicotinamide binding site of tankyrase 2. Potencies of the active flavones toward tankyrases vary between 50 nM and 1.1 μM, and flavones show up to 200-fold selectivity for tankyrases over ARTD1. The molecular details of the interactions revealed by cocrystal structures efficiently describe the properties of potent flavone derivatives inhibiting tankyrases.


    Organizational Affiliation

    Biocenter Oulu and Department of Biochemistry, University of Oulu, Oulu, 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
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
16S
Query on 16S

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Download CCD File 
A, B
2-(3,4-dihydroxyphenyl)-4H-chromen-4-one
3',4'-Dihydroxyflavone
C15 H10 O4
SRNPMQHYWVKBAV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
16SIC50: 170 nM (100) BINDINGDB
16SIC50: 170 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 93.970α = 90.00
b = 95.570β = 90.00
c = 118.250γ = 90.00
Software Package:
Software NamePurpose
MxCuBEdata collection
XSCALEdata scaling
MOLREPphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-31
    Type: Initial release
  • Version 1.1: 2013-05-08
    Type: Database references
  • Version 1.2: 2013-05-22
    Type: Database references