7R5X | pdb_00007r5x

Tankyrase 2 in complex with an inhibitor (OUL211)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.224 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.194 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7R5X

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

[1,2,4]Triazolo[3,4- b ]benzothiazole Scaffold as Versatile Nicotinamide Mimic Allowing Nanomolar Inhibition of Different PARP Enzymes.

Murthy, S.Nizi, M.G.Maksimainen, M.M.Massari, S.Alaviuhkola, J.Lippok, B.E.Vagaggini, C.Sowa, S.T.Galera-Prat, A.Ashok, Y.Venkannagari, H.Prunskaite-Hyyrylainen, R.Dreassi, E.Luscher, B.Korn, P.Tabarrini, O.Lehtio, L.

(2023) J Med Chem 66: 1301-1320

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c01460
  • Primary Citation Related Structures: 
    7R3L, 7R3O, 7R3Z, 7R4A, 7R59, 7R5D, 7R5X, 7Z1V, 7Z1W, 7Z1Y, 7Z2O, 7Z2Q, 7Z41

  • PubMed Abstract: 

    We report [1,2,4]triazolo[3,4- b ]benzothiazole (TBT) as a new inhibitor scaffold, which competes with nicotinamide in the binding pocket of human poly- and mono-ADP-ribosylating enzymes. The binding mode was studied through analogues and cocrystal structures with TNKS2, PARP2, PARP14, and PARP15. Based on the substitution pattern, we were able to identify 3-amino derivatives 21 (OUL243) and 27 (OUL232) as inhibitors of mono-ARTs PARP7, PARP10, PARP11, PARP12, PARP14, and PARP15 at nM potencies, with 27 being the most potent PARP10 inhibitor described to date (IC 50 of 7.8 nM) and the first PARP12 inhibitor ever reported. On the contrary, hydroxy derivative 16 (OUL245) inhibits poly-ARTs with a selectivity toward PARP2. The scaffold does not possess inherent cell toxicity, and the inhibitors can enter cells and engage with the target protein. This, together with favorable ADME properties, demonstrates the potential of TBT scaffold for future drug development efforts toward selective inhibitors against specific enzymes.


  • Organizational Affiliation
    • Faculty of Biochemistry and Molecular Medicine and Biocenter Oulu, University of Oulu, Oulu90220, Finland.

Macromolecule Content 

  • Total Structure Weight: 50.68 kDa 
  • Atom Count: 3,631 
  • Modeled Residue Count: 419 
  • Deposited Residue Count: 438 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase tankyrase-2A [auth AAA],
C [auth BBB]
171Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase tankyrase-2B [auth A],
D [auth B]
48Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (PDB Primary Data)
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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I6D
(Subject of Investigation/LOI)

Query on I6D



Download:Ideal Coordinates CCD File
E [auth AAA],
J [auth BBB]
7-methyl-[1,2,4]triazolo[3,4-b][1,3]benzothiazole
C9 H7 N3 S
AYAUSTLAUXOBIN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth AAA],
H [auth AAA],
L [auth BBB],
M [auth BBB]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



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

Query on ZN



Download:Ideal Coordinates CCD File
F [auth AAA],
K [auth BBB]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
I6D BindingDB:  7R5X IC50: 950 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.224 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.194 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.94α = 90
b = 96.99β = 90
c = 119.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland287063
Academy of FinlandFinland294085

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2024-02-07
    Changes: Data collection, Refinement description