5NSP | pdb_00005nsp

Crystal structure of TNKS2 in complex with OD334


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5NSP

Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 55.86 kDa 
  • Atom Count: 3,524 
  • Modeled Residue Count: 417 
  • Deposited Residue Count: 480 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2A,
C [auth B]
191Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens)
Explore Q9H2K2 
Go to UniProtKB:  Q9H2K2
PHAROS:  Q9H2K2
GTEx:  ENSG00000107854 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2K2
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2B [auth C],
D
49Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H2K2 (Homo sapiens)
Explore Q9H2K2 
Go to UniProtKB:  Q9H2K2
PHAROS:  Q9H2K2
GTEx:  ENSG00000107854 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2K2
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
97E

Query on 97E



Download:Ideal Coordinates CCD File
M [auth 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
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
H [auth C],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
I [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
BCT

Query on BCT



Download:Ideal Coordinates CCD File
G [auth A],
N [auth B]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.247 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.06α = 90
b = 98.14β = 90
c = 119.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biocenter OuluFinland--

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: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description