5NSP

Crystal structure of TNKS2 in complex with OD334


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of a Novel Series of Tankyrase Inhibitors by a Hybridization Approach.

Anumala, U.R.Waaler, J.Nkizinkiko, Y.Ignatev, A.Lazarow, K.Lindemann, P.Olsen, P.A.Murthy, S.Obaji, E.Majouga, A.G.Leonov, S.von Kries, J.P.Lehtio, L.Krauss, S.Nazare, M.

(2017) J. Med. Chem. 60: 10013-10025

  • DOI: 10.1021/acs.jmedchem.7b00883
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A structure-guided hybridization approach using two privileged substructures gave instant access to a new series of tankyrase inhibitors. The identified inhibitor 16 displays high target affinity on tankyrase 1 and 2 with biochemical and cellular IC5 ...

    A structure-guided hybridization approach using two privileged substructures gave instant access to a new series of tankyrase inhibitors. The identified inhibitor 16 displays high target affinity on tankyrase 1 and 2 with biochemical and cellular IC50 values of 29 nM, 6.3 nM and 19 nM, respectively, and high selectivity toward other poly (ADP-ribose) polymerase enzymes. The identified inhibitor shows a favorable in vitro ADME profile as well as good oral bioavailability in mice, rats, and dogs. Critical for the approach was the utilization of an appropriate linker between 1,2,4-triazole and benzimidazolone moieties, whereby a cyclobutyl linker displayed superior affinity compared to a cyclohexane and phenyl linker.


    Organizational Affiliation

    Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Campus Berlin-Buch, 13125 Berlin, Germany.




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 5 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, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
BCT
Query on BCT

Download SDF File 
Download CCD File 
A, B
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
97E
Query on 97E

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Download CCD File 
B
1-[4-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]phenyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile
C26 H15 Cl N8 O
GQOVEMXVWLBEGU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.190 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 90.060α = 90.00
b = 98.140β = 90.00
c = 119.510γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biocenter OuluFinland--

Revision History 

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references