7OM1 | pdb_00007om1

Tankyrase 2 in complex with an inhibitor (OUL220)

• PDB DOI: https://doi.org/10.2210/pdb7OM1/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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.190 (DCC) 

Starting Model: experimental

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 
• DOI: https://doi.org/10.1016/j.bmc.2021.116511
• Primary Citation 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.

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Organizational Affiliation: 
• Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland.
Research Unit of Sustainable Chemistry, Faculty of Technology, University of Oulu, Oulu, Finland.
Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.85 kDa 
• Atom Count: 3,811 
• Modeled Residue Count: 419 
• Deposited Residue Count: 438 
• Unique protein chains: 2

Macromolecules

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 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1OI (Subject of Investigation/LOI)	E [auth AAA], K [auth BBB]	8-methoxy-4~{H}-thieno[2,3-c]isoquinolin-5-one C12 H9 N O2 S HTTRFYNWHOXUPE-UHFFFAOYSA-N
SO4	G [auth AAA], I [auth A], M [auth BBB], N [auth BBB]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], J [auth BBB]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	F [auth AAA], L [auth BBB]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1OI	BindingDB:  7OM1	IC50: 138 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.197 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.190 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.21	α = 90
b = 98.3	β = 90
c = 118.27	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-08 
Deposition Author(s): Sowa, S.T., Lehtio, L.

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

Revision History  

• Version 1.0: 2021-12-08
  Type: Initial release
  
• Version 1.1: 2021-12-22
  Changes: Database references
• Version 1.2: 2022-03-16
  Changes: Source and taxonomy
• Version 1.3: 2024-01-31
  Changes: Data collection, Derived calculations, Refinement description