4PNQ | pdb_00004pnq

Crystal Structure of human Tankyrase 2 in complex with 5AIQ.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.227 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.188 (Depositor) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4PNQ

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Insights into the binding of PARP inhibitors to the catalytic domain of human tankyrase-2.

Qiu, W.Lam, R.Voytyuk, O.Romanov, V.Gordon, R.Gebremeskel, S.Vodsedalek, J.Thompson, C.Beletskaya, I.Battaile, K.P.Pai, E.F.Rottapel, R.Chirgadze, N.Y.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2740-2753

  • DOI: https://doi.org/10.1107/S1399004714017660
  • Primary Citation Related Structures: 
    4PML, 4PNL, 4PNM, 4PNN, 4PNQ, 4PNR, 4PNS, 4PNT, 4TJU, 4TJW, 4TJY, 4TK0, 4TK5, 4TKF, 4TKG, 4TKI

  • PubMed Abstract: 

    The poly(ADP-ribose) polymerase (PARP) family represents a new class of therapeutic targets with diverse potential disease indications. PARP1 and PARP2 inhibitors have been developed for breast and ovarian tumors manifesting double-stranded DNA-repair defects, whereas tankyrase 1 and 2 (TNKS1 and TNKS2, also known as PARP5a and PARP5b, respectively) inhibitors have been developed for tumors with elevated β-catenin activity. As the clinical relevance of PARP inhibitors continues to be actively explored, there is heightened interest in the design of selective inhibitors based on the detailed structural features of how small-molecule inhibitors bind to each of the PARP family members. Here, the high-resolution crystal structures of the human TNKS2 PARP domain in complex with 16 various PARP inhibitors are reported, including the compounds BSI-201, AZD-2281 and ABT-888, which are currently in Phase 2 or 3 clinical trials. These structures provide insight into the inhibitor-binding modes for the tankyrase PARP domain and valuable information to guide the rational design of future tankyrase-specific inhibitors.


  • Organizational Affiliation
    • Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 104.75 kDa 
  • Atom Count: 7,421 
  • Modeled Residue Count: 808 
  • Deposited Residue Count: 908 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-2
A, B, C, D
227Homo sapiensMutation(s): 0 
Gene Names: TNKS2PARP5BTANK2TNKL
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2K2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
32X

Query on 32X



Download:Ideal Coordinates CCD File
F [auth A],
G [auth B],
I [auth C]
5-aminoisoquinolin-1(4H)-one
C9 H8 N2 O
UMWAQUVIYVQOLI-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth A],
H [auth B],
J [auth C],
L [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA

Query on IPA



Download:Ideal Coordinates CCD File
K [auth C]ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.227 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.188 (Depositor) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.03α = 90
b = 79.47β = 90
c = 153.45γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2023-12-27
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy