5AL3

Crystal structure of TNKS2 in complex with 2-(2,4-dichlorophenyl)-1- methyl-1H,2H,3H,4H-pyrido(2,3-d)pyrimidin-4-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Discovery of Potent and Selective Nonplanar Tankyrase Inhibiting Nicotinamide Mimics.

Nkizinkiko, Y.Suneel Kumar, B.V.S.Jeankumar, V.U.Haikarainen, T.Koivunen, J.Madhuri, C.Yogeeswari, P.Venkannagari, H.Obaji, E.Pihlajaniemi, T.Sriram, D.Lehtio, L.

(2015) Bioorg Med Chem 23: 4139

  • DOI: https://doi.org/10.1016/j.bmc.2015.06.063
  • Primary Citation of Related Structures:  
    5AKU, 5AKW, 5AL1, 5AL2, 5AL3, 5AL4, 5AL5

  • PubMed Abstract: 

    Diphtheria toxin-like ADP-ribosyltransferases catalyse a posttranslational modification, ADP-ribosylation and form a protein family of 17 members in humans. Two of the family members, tankyrases 1 and 2, are involved in several cellular processes including mitosis and Wnt/β-catenin signalling pathway. They are often over-expressed in cancer cells and have been linked with the survival of cancer cells making them potential therapeutic targets. In this study, we identified nine tankyrase inhibitors through virtual and in vitro screening. Crystal structures of tankyrase 2 with the compounds showed that they bind to the nicotinamide binding site of the catalytic domain. Based on the co-crystal structures we designed and synthesized a series of tetrahydroquinazolin-4-one and pyridopyrimidin-4-one analogs and were subsequently able to improve the potency of a hit compound almost 100-fold (from 11 μM to 150 nM). The most potent compounds were selective towards tankyrases over a panel of other human ARTD enzymes. They also inhibited Wnt/β-catenin pathway in a cell-based reporter assay demonstrating the potential usefulness of the identified new scaffolds for further development.


  • Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, PO Box 5400, FIN-90014 Oulu, Finland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TANKYRASE 2
A, B
240Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H2K2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TGW
Query on TGW

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
(2R)-2-(2,4-dichlorophenyl)-1-methyl-2,3-dihydropyrido[2,3-d]pyrimidin-4-one
C14 H11 Cl2 N3 O
REZFMSXTMURZKT-CYBMUJFWSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A],
M [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TGW BindingDB:  5AL3 IC50: min: 1.00e+4, max: 1.10e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.62α = 90
b = 98.57β = 90
c = 118.76γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description