7OMC

Tankyrase 2 in complex with an inhibitor (OUL228)

PDB DOI: https://doi.org/10.2210/pdb7OMC/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-05-21 Released: 2021-12-08
Deposition Author(s): Sowa, S.T., Lehtio, L.
Funding Organization(s): Academy of Finland, Sigrid Juselius Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226
R-Value Work: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Analogs of TIQ-A as inhibitors of human mono-ADP-ribosylating PARPs.

Maksimainen, M.M., Murthy, S., Sowa, S.T., Galera-Prat, A., Rolina, E., Heiskanen, J.P., Lehtio, L.

(2021) Bioorg Med Chem 52: 116511-116511

PubMed: 34801828 Search on PubMed
DOI: https://doi.org/10.1016/j.bmc.2021.116511
Primary Citation of Related Structures:
7OLJ, 7OM1, 7OMC, 7OQQ, 7OSP, 7OSS, 7OSX, 7OTF, 7OTH, 7OUW, 7OUX

PubMed Abstract:
The scaffold of TIQ-A, a previously known inhibitor of human poly-ADP-ribosyltransferase PARP1, was utilized to develop inhibitors against human mono-ADP-ribosyltransferases through structure-guided design and activity profiling. By supplementing the TIQ-A scaffold with small structural changes, based on a PARP10 inhibitor OUL35, selectivity changed from poly-ADP-ribosyltransferases towards mono-ADP-ribosyltransferases. Binding modes of analogs were experimentally verified by determining complex crystal structures with mono-ADP-ribosyltransferase PARP15 and with poly-ADP-ribosyltransferase TNKS2. The best analogs of the study achieved 10-20-fold selectivity towards mono-ADP-ribosyltransferases PARP10 and PARP15 while maintaining micromolar potencies. The work demonstrates a route to differentiate compound selectivity between mono- and poly-ribosyltransferases of the human ARTD family.

Organizational Affiliation

Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.

Macromolecule Content

Total Structure Weight: 50.82 kDa
Atom Count: 3,622
Modelled Residue Count: 414
Deposited Residue Count: 438
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase tankyrase-2	A [auth AAA], C [auth BBB]	171	Homo sapiens	Mutation(s): 0 Gene Names: TNKS2, PARP5B, TANK2, TNKL 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H2K2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase tankyrase-2	B [auth A], D [auth B]	48	Homo sapiens	Mutation(s): 0 Gene Names: TNKS2, PARP5B, TANK2, TNKL 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9H2K2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VJN (Subject of Investigation/LOI) Query on VJN Download Ideal Coordinates CCD File SDF format, chain E [auth AAA] SDF format, chain J [auth BBB] MOL2 format, chain E [auth AAA] MOL2 format, chain J [auth BBB]	E [auth AAA], J [auth BBB]	8-propan-2-yloxy-4~{H}-thieno[2,3-c]isoquinolin-5-one C₁₄ H₁₃ N O₂ S RRNITWOICYYQGQ-UHFFFAOYSA-N		Interactions Focus chain E [auth AAA] Focus chain J [auth BBB] Interactions & Density Focus chain E [auth AAA] Focus chain J [auth BBB]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth AAA] SDF format, chain H [auth AAA] SDF format, chain L [auth BBB] SDF format, chain M [auth BBB] MOL2 format, chain G [auth AAA] MOL2 format, chain H [auth AAA] MOL2 format, chain L [auth BBB] MOL2 format, chain M [auth BBB]	G [auth AAA], H [auth AAA], L [auth BBB], M [auth BBB]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB] Interactions & Density Focus chain G [auth AAA] Focus chain H [auth AAA] Focus chain L [auth BBB] Focus chain M [auth BBB]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth AAA] SDF format, chain K [auth BBB] MOL2 format, chain F [auth AAA] MOL2 format, chain K [auth BBB]	F [auth AAA], K [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth AAA] Focus chain K [auth BBB] Interactions & Density Focus chain F [auth AAA] Focus chain K [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.226
R-Value Work: 0.181
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.69	α = 90
b = 98.18	β = 90
c = 117.48	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-12-08

Deposition Author(s):

Sowa, S.T.

Lehtio, L.

Funding Organization	Location	Grant Number
Academy of Finland	Finland	287063, 294085
Sigrid Juselius Foundation	Finland	--

Revision History (Full details and data files)

Version 1.0: 2021-12-08
Type: Initial release
Version 1.1: 2022-03-16
Changes: Source and taxonomy
Version 1.2: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description