4I9I | pdb_00004i9i

Crystal structure of tankyrase 1 with compound 4

PDB DOI: https://doi.org/10.2210/pdb4I9I/pdb

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

Deposited: 2012-12-05 Released: 2013-02-06
Deposition Author(s): Huang, X.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.286 (Depositor), 0.265 (DCC)
R-Value Work:
0.250 (Depositor), 0.236 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Discovery of a class of novel tankyrase inhibitors that bind to both the nicotinamide pocket and the induced pocket.

Bregman, H., Gunaydin, H., Gu, Y., Schneider, S., Wilson, C., DiMauro, E.F., Huang, X.

(2013) J Med Chem 56: 1341-1345

PubMed: 23316926 Search on PubMed
DOI: https://doi.org/10.1021/jm301607v
Primary Citation of Related Structures:
4I9I

PubMed Abstract:
Potent and selective inhibitors of tankyrases have recently been characterized to bind to an induced pocket. Here we report the identification of a novel potent and selective tankyrase inhibitor that binds to both the nicotinamide pocket and the induced pocket. The crystal structure of human TNKS1 in complex with this "dual-binder" provides a molecular basis for their strong and specific interactions and suggests clues for the further development of tankyrase inhibitors.

Organizational Affiliation

Department of Medicinal Chemistry, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, USA.

Macromolecule Content

Total Structure Weight: 102.2 kDa
Atom Count: 7,021
Modeled Residue Count: 838
Deposited Residue Count: 868
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, C, D	217	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1DY Query on 1DY Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], L [auth D]	N-(2-methoxyphenyl)-4-{[3-(4-oxo-3,4-dihydroquinazolin-2-yl)propanoyl]amino}benzamide C₂₅ H₂₂ N₄ O₄ WWKKOAKRYQQEBT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain K [auth D] SDF format, chain I [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain K [auth D] MOL2 format, chain I [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain K [auth D] mmCIF format, chain I [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
1DY	BindingDB: 4I9I	IC50: min: 2, max: 8 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.286 (Depositor), 0.265 (DCC)
R-Value Work: 0.250 (Depositor), 0.236 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.622	α = 90
b = 77.122	β = 90
c = 84.507	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Huang, X.

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2013-05-22
Changes: Database references
Version 1.2: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary