5NOB | pdb_00005nob

Crystal structure of human tankyrase 2 in complex with OD336

• PDB DOI: https://doi.org/10.2210/pdb5NOB/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-04-11 Released: 2017-11-29 
• Deposition Author(s): Ignatev, A., Lehtio, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

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

• PubMed: 29155568 
• 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.

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Organizational Affiliation: 
• Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) , Campus Berlin-Buch, 13125 Berlin, Germany.
Unit for Cell Signaling, Institute of Medical Microbiology, Oslo University Hospital , Gaustadalleen 34, 0372 Oslo, Norway.
Hybrid Technology Hub, Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo , 0372 Oslo, Norway.
Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu , P.O. Box 5400, 90014 Oulu, Finland.
Department of Chemistry, Moscow State University , Leninskie Gory 1/3, Moscow 119991, Russia.
National University of Science and Technology MISiS , Leninsky Avenue 4, Moscow 119049, Russia.
Moscow Institute of Physics and Technology (State University) , Institutskiy Lane 9, 141700 Dolgoprudny, Russia.
Berlin Institute of Health (BIH) , Anna-Louisa-Karsch-Strasse 2, 10178 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 55.67 kDa 
• Atom Count: 3,536 
• Modeled Residue Count: 405 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	A, B	240	Homo sapiens	Mutation(s): 0  Gene Names: TNKS2, PARP5B, TANK2, TNKL 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
92T	C [auth A], E [auth B]	1-[3-[4-(2-chlorophenyl)-5-pyrimidin-4-yl-1,2,4-triazol-3-yl]cyclobutyl]-2-oxidanylidene-3~{H}-benzimidazole-5-carbonitrile C24 H17 Cl N8 O MYNRZMIPPXBMLY-WKILWMFISA-N
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.237 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.58	α = 90
b = 75.52	β = 90
c = 148.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-11-29 
Deposition Author(s): Ignatev, A., Lehtio, L.

Revision History  

• Version 1.0: 2017-11-29
  Type: Initial release
  
• Version 1.1: 2018-01-10
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description