5NOB

Crystal structure of human tankyrase 2 in complex with OD336


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1021/acs.jmedchem.7b00883
  • Primary Citation of Related Structures:  
    5NOB, 5NSP

  • 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 IC 50 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tankyrase-2
A, B
240Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens)
Go to UniProtKB:  Q9H2K2
PHAROS:  Q9H2K2
GTEx:  ENSG00000107854 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
92T
Query on 92T

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile
C24 H17 Cl N8 O
MYNRZMIPPXBMLY-WKILWMFISA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
92T BindingDB:  5NOB IC50: min: 1.1, max: 977 (nM) from 8 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.58α = 90
b = 75.52β = 90
c = 148.12γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-29
    Type: Initial release
  • Version 1.1: 2018-01-10
    Changes: Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description