5EBT | pdb_00005ebt

Tankyrase 1 with Phthalazinone 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 
    0.208 (Depositor), 0.201 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5EBT

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of AZ0108, an orally bioavailable phthalazinone PARP inhibitor that blocks centrosome clustering.

Johannes, J.W.Almeida, L.Daly, K.Ferguson, A.D.Grosskurth, S.E.Guan, H.Howard, T.Ioannidis, S.Kazmirski, S.Lamb, M.L.Larsen, N.A.Lyne, P.D.Mikule, K.Ogoe, C.Peng, B.Petteruti, P.Read, J.A.Su, N.Sylvester, M.Throner, S.Wang, W.Wang, X.Wu, J.Ye, Q.Yu, Y.Zheng, X.Scott, D.A.

(2015) Bioorg Med Chem Lett 25: 5743-5747

  • DOI: https://doi.org/10.1016/j.bmcl.2015.10.079
  • Primary Citation Related Structures: 
    5EBT, 5ECE

  • PubMed Abstract: 

    The propensity for cancer cells to accumulate additional centrosomes relative to normal cells could be exploited for therapeutic benefit in oncology. Following literature reports that suggested TNKS1 (tankyrase 1) and PARP16 may be involved with spindle structure and function and may play a role in suppressing multi-polar spindle formation in cells with supernumerary centrosomes, we initiated a phenotypic screen to look for small molecule poly (ADP-ribose) polymerase (PARP) enzyme family inhibitors that could produce a multi-polar spindle phenotype via declustering of centrosomes. Screening of AstraZeneca's collection of phthalazinone PARP inhibitors in HeLa cells using high-content screening techniques identified several compounds that produced a multi-polar spindle phenotype at low nanomolar concentrations. Characterization of these compounds across a broad panel of PARP family enzyme assays indicated that they had activity against several PARP family enzymes, including PARP1, 2, 3, 5a, 5b, and 6. Further optimization of these initial hits for improved declustering potency, solubility, permeability, and oral bioavailability resulted in AZ0108, a PARP1, 2, 6 inhibitor that potently inhibits centrosome clustering and is suitable for in vivo efficacy and tolerability studies.


  • Organizational Affiliation
    • AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, MA 02451, United States.

Macromolecule Content 

  • Total Structure Weight: 99.02 kDa 
  • Atom Count: 7,283 
  • Modeled Residue Count: 832 
  • Deposited Residue Count: 840 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tankyrase-1
A, B, C, D
210Homo sapiensMutation(s): 0 
Gene Names: TNKSPARP5APARPLTIN1TINF1TNKS1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95271
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5N8

Query on 5N8



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
K [auth C],
N [auth D]
4-[bis(fluoranyl)-[3-[[(6~{S})-6-methyl-3-(trifluoromethyl)-6,8-dihydro-5~{H}-[1,2,4]triazolo[4,3-a]pyrazin-7-yl]carbonyl]phenyl]methyl]-2~{H}-phthalazin-1-one
C23 H17 F5 N6 O2
SRNBPLVNLYRSLY-LBPRGKRZSA-N
BU3

Query on BU3



Download:Ideal Coordinates CCD File
E [auth A],
J [auth C]
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
L [auth C],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free:  0.208 (Depositor), 0.201 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.733α = 90
b = 151.189β = 96.28
c = 57.224γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-02
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations