4BFP | pdb_00004bfp

Crystal structure of human tankyrase 2 in complex with WIKI4

PDB DOI: https://doi.org/10.2210/pdb4BFP/pdb

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

Deposited: 2013-03-21 Released: 2013-06-19
Deposition Author(s): Haikarainen, T., Narwal, M., Lehtio, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.250 (Depositor), 0.255 (DCC)
R-Value Work:
0.202 (Depositor), 0.208 (DCC)
R-Value Observed:
0.204 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Structural Basis and Selectivity of Tankyrase Inhibition by a Wnt Signaling Inhibitor Wiki4

Haikarainen, T., Venkannagari, H., Narwal, M., Obaji, E., Lee, H., Nkizinkiko, Y., Lehtio, L.

(2013) PLoS One 8: 65404

PubMed: 23762361 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pone.0065404
Primary Citation Related Structures:
4BFP

PubMed Abstract:
Recently a novel inhibitor of Wnt signaling was discovered. The compound, WIKI4, was found to act through tankyrase inhibition and regulate β-catenin levels in many cancer cell lines and human embryonic stem cells. Here we confirm that WIKI4 is a high potency tankyrase inhibitor and that it selectively inhibits tankyrases over other ARTD enzymes tested. The binding mode of the compound to tankyrase 2 was determined by protein X-ray crystallography to 2.4 Å resolution. The structure revealed a novel binding mode to the adenosine subsite of the donor NAD(+) binding groove of the catalytic domain. Our results form a structural basis for further development of potent and selective tankyrase inhibitors based on the WIKI4 scaffold.

Organizational Affiliation

Biocenter Oulu, Department of Biochemistry, University of Oulu, Oulu, Finland.

Macromolecule Content

Total Structure Weight: 56.16 kDa
Atom Count: 3,571
Modeled Residue Count: 417
Deposited Residue Count: 480
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TANKYRASE-2	A, B	240	Homo sapiens	Mutation(s): 0 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
SWY Query on SWY Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	2-[3-[[4-(4-methoxyphenyl)-5-pyridin-4-yl-1,2,4-triazol-3-yl]sulfanyl]propyl]benzo[de]isoquinoline-1,3-dione C₂₉ H₂₃ N₅ O₃ S RNUXIZKXJOGYQP-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], H [auth B], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A]	F [auth A], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.250 (Depositor), 0.255 (DCC)
R-Value Work: 0.202 (Depositor), 0.208 (DCC)
R-Value Observed: 0.204 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.96	α = 90
b = 93.17	β = 90
c = 117.05	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Haikarainen, T.

Narwal, M.

Lehtio, L.

Revision History (Full details and data files)

Version 1.0: 2013-06-19
Type: Initial release
Version 1.1: 2013-06-26
Changes: Database references
Version 1.2: 2014-09-10
Changes: Database references
Version 1.3: 2015-04-01
Changes: Database references
Version 1.4: 2019-01-30
Changes: Data collection, Experimental preparation
Version 1.5: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.6: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other