4KRS

Tankyrase-1 complexed with small molecule inhibitor

PDB DOI: https://doi.org/10.2210/pdb4KRS/pdb

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

Deposited: 2013-05-17 Released: 2013-08-28
Deposition Author(s): Stams, T., Kirby, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.269
R-Value Work: 0.207
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure-Efficiency Relationship of [1,2,4]Triazol-3-ylamines as Novel Nicotinamide Isosteres that Inhibit Tankyrases.

Shultz, M.D., Majumdar, D., Chin, D.N., Fortin, P.D., Feng, Y., Gould, T., Kirby, C.A., Stams, T., Waters, N.J., Shao, W.

(2013) J Med Chem 56: 7049-7059

PubMed: 23879431 Search on PubMed
DOI: https://doi.org/10.1021/jm400826j
Primary Citation of Related Structures:
4KRS

PubMed Abstract:
Tankyrases 1 and 2 are members of the poly(ADP-ribose) polymerase (PARP) family of enzymes that modulate Wnt pathway signaling. While amide- and lactam-based nicotinamide mimetics that inhibit tankyrase activity, such as XAV939, are well-known, herein we report the discovery and evaluation of a novel nicotinamide isostere that demonstrates selectivity over other PARP family members. We demonstrate the utilization of lipophilic efficiency-based structure-efficiency relationships (SER) to rapidly drive the evaluation of this series. These efforts led to a series of selective, cell-active compounds with solubility, physicochemical, and in vitro properties suitable for further optimization.

Organizational Affiliation

Novartis Institutes for Biomedical Research Incorporated , 250 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States.

Macromolecule Content

Total Structure Weight: 51.92 kDa
Atom Count: 3,525
Modelled Residue Count: 412
Deposited Residue Count: 446
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tankyrase-1	A, B	223	Homo sapiens	Mutation(s): 0 Gene Names: TNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1 EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95271 (Homo sapiens) Explore O95271 Go to UniProtKB: O95271
PHAROS: O95271 GTEx: ENSG00000173273
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95271
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1SX Query on 1SX Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	H [auth A], K [auth B]	4-tert-butyl-N-(5,6-dihydro[1,3]thiazolo[2,3-c][1,2,4]triazol-3-yl)benzamide C₁₅ H₁₈ N₄ O S VNFVQSRTHCEODA-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B]	D [auth A], E [auth A], F [auth A], G [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
1SX	PDBBind: 4KRS	IC50: 299 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.269
R-Value Work: 0.207
R-Value Observed: 0.210
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.594	α = 90
b = 44.233	β = 90.14
c = 87.845	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-08-28

Deposition Author(s):

Stams, T.

Kirby, C.

Revision History (Full details and data files)

Version 1.0: 2013-08-28
Type: Initial release
Version 1.1: 2013-09-25
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2024-02-28
Changes: Data collection, Database references, Derived calculations