4M7B | pdb_00004m7b

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.

Experimental Data Snapshot

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jm401356t
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 (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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9H2K2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28C Query on 28C Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain D [auth A] MOL2 format, chain H [auth C] MOL2 format, chain D [auth A] mmCIF format, chain H [auth C] mmCIF format, chain D [auth A]	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		Interactions Focus chain D [auth A] Focus chain H [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C]	E [auth A], F [auth A], I [auth C], J [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth C] Focus chain J [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain C [auth A] MOL2 format, chain G [auth C] MOL2 format, chain C [auth A] mmCIF format, chain G [auth C] mmCIF format, chain C [auth A]	C [auth A], G [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth C] Interactions & Density Focus chain C [auth A] Focus chain G [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
28C	BindingDB: 4M7B	IC50: min: 12, max: 200 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

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

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Karlberg, T.

Camaioni, E.

Schuler, H.

Revision History (Full details and data files)

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