5AKW

Crystal structure of TNKS2 in complex with 2-(4-chlorophenyl)-1,2,3,4- tetrahydroquinazolin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of Potent and Selective Nonplanar Tankyrase Inhibiting Nicotinamide Mimics.

Nkizinkiko, Y.Suneel Kumar, B.V.S.Jeankumar, V.U.Haikarainen, T.Koivunen, J.Madhuri, C.Yogeeswari, P.Venkannagari, H.Obaji, E.Pihlajaniemi, T.Sriram, D.Lehtio, L.

(2015) Bioorg.Med.Chem. 23: 4139

  • DOI: 10.1016/j.bmc.2015.06.063
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diphtheria toxin-like ADP-ribosyltransferases catalyse a posttranslational modification, ADP-ribosylation and form a protein family of 17 members in humans. Two of the family members, tankyrases 1 and 2, are involved in several cellular processes inc ...

    Diphtheria toxin-like ADP-ribosyltransferases catalyse a posttranslational modification, ADP-ribosylation and form a protein family of 17 members in humans. Two of the family members, tankyrases 1 and 2, are involved in several cellular processes including mitosis and Wnt/β-catenin signalling pathway. They are often over-expressed in cancer cells and have been linked with the survival of cancer cells making them potential therapeutic targets. In this study, we identified nine tankyrase inhibitors through virtual and in vitro screening. Crystal structures of tankyrase 2 with the compounds showed that they bind to the nicotinamide binding site of the catalytic domain. Based on the co-crystal structures we designed and synthesized a series of tetrahydroquinazolin-4-one and pyridopyrimidin-4-one analogs and were subsequently able to improve the potency of a hit compound almost 100-fold (from 11 μM to 150 nM). The most potent compounds were selective towards tankyrases over a panel of other human ARTD enzymes. They also inhibited Wnt/β-catenin pathway in a cell-based reporter assay demonstrating the potential usefulness of the identified new scaffolds for further development.


    Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland.,Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India. Electronic address: dsriram@hyderabad.bits-pilani.ac.in.,Department of Pharmacy at Birla Institute of Technology and Science-Pilani, Hyderabad campus, Hyderabad 500078, India.,Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland. Electronic address: lari.lehtio@oulu.fi.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TANKYRASE-2
A, B
240Homo 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

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NKI
Query on NKI

Download SDF File 
Download CCD File 
A, B
(2S)-2-(4-chlorophenyl)-2,3-dihydro-1H-quinazolin-4-one
C14 H11 Cl N2 O
FPWIEUZTQYJRJZ-ZDUSSCGKSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NKIIC50: 410 - 417 nM (92) BINDINGDB
NKIIC50: 410 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.910α = 90.00
b = 98.310β = 90.00
c = 119.250γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
XSCALEdata scaling
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references