4M7B

Human tankyrase 2 - catalytic Parp domain in complex with an inhibitor UPF1854

• PDB DOI: https://doi.org/10.2210/pdb4M7B/pdb

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


• Deposited: 2013-08-12 Released: 2014-03-12 
• Deposition Author(s): Karlberg, T., Camaioni, E., Schuler, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Literature

Design, Synthesis, Crystallographic Studies, and Preliminary Biological Appraisal of New Substituted Triazolo[4,3-b]pyridazin-8-amine Derivatives as Tankyrase Inhibitors.

Liscio, P., Carotti, A., Asciutti, S., Karlberg, T., Bellocchi, D., Llacuna, L., Macchiarulo, A., Aaronson, S.A., Schuler, H., Pellicciari, R., Camaioni, E.

(2014) J Med Chem 57: 2807-2812

• PubMed: 24527792 
• DOI: https://doi.org/10.1021/jm401356t
• Primary Citation of Related Structures:  
  4M7B


• PubMed Abstract: 
  

  Searching for selective tankyrases (TNKSs) inhibitors, a new small series of 6,8-disubstituted triazolo[4,3-b]piridazines has been synthesized and characterized biologically. Structure-based optimization of the starting hit compound NNL (3) prompted us to the discovery of 4-(2-(6-methyl-[1,2,4]triazolo[4,3-b]pyridazin-8-ylamino)ethyl)phenol (12), a low nanomolar selective TNKSs inhibitor working as NAD isostere as ascertained by crystallographic analysis. Preliminary biological data candidate this new class of derivatives as a powerful pharmacological tools in the unraveling of TNKS implications in physiopathological conditions.

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Organizational Affiliation: 

Dipartimento di Chimica e Tecnologia del Farmaco, Università degli Studi di Perugia , Via del Liceo 1, 06123 Perugia, Italy.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 55.65 kDa 
• Atom Count: 3,609 
• Modelled Residue Count: 412 
• Deposited Residue Count: 480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-2	A, B [auth C]	240	Homo sapiens	Mutation(s): 0  Gene Names: PARP5B, TANK2, TNKL, TNKS2 EC: 2.4.2.30
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
28C	D [auth A], H [auth C]	4-{2-[(6-methyl[1,2,4]triazolo[4,3-b]pyridazin-8-yl)amino]ethyl}phenol C14 H15 N5 O IRYZTIMDNVDWKI-UHFFFAOYSA-N
SO4	E [auth A], F [auth A], I [auth C], J [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
28C	BindingDB:  4M7B	IC50: 200 (nM) from 1 assay(s)
	Binding MOAD:  4M7B	IC50: 200 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.226 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.741	α = 90
b = 96.734	β = 90
c = 118.606	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-03-12 
Deposition Author(s): Karlberg, T., Camaioni, E., Schuler, H.

Revision History  

• Version 1.0: 2014-03-12
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description