7O6X | pdb_00007o6x

Tankyrase 2 in complex with an inhibitor (OM-153)

• PDB DOI: https://doi.org/10.2210/pdb7O6X/pdb

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


• Deposited: 2021-04-12 Released: 2022-01-12 
• Deposition Author(s): Sowa, S.T., Lehtio, L.
• Funding Organization(s): Academy of Finland, Jane and Aatos Erkko Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.217 (DCC) 

Starting Model: experimental

Literature

Development of a 1,2,4-Triazole-Based Lead Tankyrase Inhibitor: Part II.

Leenders, R.G.G., Brinch, S.A., Sowa, S.T., Amundsen-Isaksen, E., Galera-Prat, A., Murthy, S., Aertssen, S., Smits, J.N., Nieczypor, P., Damen, E., Wegert, A., Nazare, M., Lehtio, L., Waaler, J., Krauss, S.

(2021) J Med Chem 64: 17936-17949

• PubMed: 34878777 
• DOI: https://doi.org/10.1021/acs.jmedchem.1c01264
• Primary Citation Related Structures: 
  7O6X


• PubMed Abstract: 
  

  Tankyrase 1 and 2 (TNKS1/2) catalyze post-translational modification by poly-ADP-ribosylation of a plethora of target proteins. In this function, TNKS1/2 also impact the WNT/β-catenin and Hippo signaling pathways that are involved in numerous human disease conditions including cancer. Targeting TNKS1/2 with small-molecule inhibitors shows promising potential to modulate the involved pathways, thereby potentiating disease intervention. Based on our 1,2,4-triazole-based lead compound 1 (OM-1700), further structure-activity relationship analyses of East-, South- and West-single-point alterations and hybrids identified compound 24 (OM-153). Compound 24 showed picomolar IC ₅₀ inhibition in a cellular (HEK293) WNT/β-catenin signaling reporter assay, no off-target liabilities, overall favorable absorption, distribution, metabolism, and excretion (ADME) properties, and an improved pharmacokinetic profile in mice. Moreover, treatment with compound 24 induced dose-dependent biomarker engagement and reduced cell growth in the colon cancer cell line COLO 320DM.

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Organizational Affiliation: 
• Symeres, Kerkenbos 1013, 6546 BB Nijmegen, The Netherlands.
Hybrid Technology Hub - Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway.
Department of Immunology and Transfusion Medicine, Oslo University Hospital, 0424 Oslo, Norway.
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, 90014 Oulu, Finland.
Medicinal Chemistry, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Campus Berlin Buch, Robert-Roessle-Str. 10, 13125 Berlin, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 50.84 kDa 
• Atom Count: 3,438 
• Modeled Residue Count: 400 
• 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 BBB], C [auth AAA]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V4Q (Subject of Investigation/LOI)	E [auth BBB], G [auth AAA]	N-[3-[5-(5-ethoxypyridin-2-yl)-4-(2-fluorophenyl)-1,2,4-triazol-3-yl]cyclobutyl]quinoxaline-5-carboxamide C28 H24 F N7 O2 ARCOJIXZDJYBCH-IYARVYRRSA-N
ZN	F [auth BBB], H [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.217 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.39	α = 90
b = 76.43	β = 90
c = 147.73	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: 2022-01-12 
Deposition Author(s): Sowa, S.T., Lehtio, L.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	287063, 294085
Jane and Aatos Erkko Foundation	Finland	--

Revision History  

• Version 1.0: 2022-01-12
  Type: Initial release
  
• Version 2.0: 2022-03-16
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2023-08-02
  Changes: Database references, Derived calculations
• Version 2.2: 2024-01-31
  Changes: Data collection, Refinement description