4GV2

Human ARTD3 (PARP3) - Catalytic domain in complex with inhibitor ME0354


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

PARP Inhibitor with Selectivity Toward ADP-Ribosyltransferase ARTD3/PARP3

Lindgren, A.E.G.Karlberg, T.Thorsell, A.G.Hesse, M.Spjut, S.Ekblad, T.Andersson, C.D.Pinto, A.F.Weigelt, J.Hottiger, M.O.Linusson, A.Elofsson, M.Schuler, H.

(2013) ACS Chem Biol 8: 1698-1703

  • DOI: 10.1021/cb4002014
  • Primary Citation of Related Structures:  
    4GV0, 4GV2, 4GV4, 4GV7

  • PubMed Abstract: 
  • Inhibiting ADP-ribosyl transferases with PARP-inhibitors is considered a promising strategy for the treatment of many cancers and ischemia, but most of the cellular targets are poorly characterized. Here, we describe an inhibitor of ADP-ribosyltransferase-3/poly(ADP-ribose) polymerase-3 (ARTD3), a regulator of DNA repair and mitotic progression ...

    Inhibiting ADP-ribosyl transferases with PARP-inhibitors is considered a promising strategy for the treatment of many cancers and ischemia, but most of the cellular targets are poorly characterized. Here, we describe an inhibitor of ADP-ribosyltransferase-3/poly(ADP-ribose) polymerase-3 (ARTD3), a regulator of DNA repair and mitotic progression. In vitro profiling against 12 members of the enzyme family suggests selectivity for ARTD3, and crystal structures illustrate the molecular basis for inhibitor selectivity. The compound is active in cells, where it elicits ARTD3-specific effects at submicromolar concentration. Our results show that by targeting the nicotinamide binding site, selective inhibition can be achieved among the closest relatives of the validated clinical target, ADP-ribosyltransferase-1/poly(ADP-ribose) polymerase-1.


    Organizational Affiliation

    Department of Chemistry, Umeå University, Umeå, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 3A357Homo sapiensMutation(s): 0 
Gene Names: PARP3ADPRT3ADPRTL3
EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F1 (Homo sapiens)
Explore Q9Y6F1 
Go to UniProtKB:  Q9Y6F1
PHAROS:  Q9Y6F1
GTEx:  ENSG00000041880 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6F1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5ME
Query on 5ME

Download Ideal Coordinates CCD File 
B [auth A]3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[(1R)-1-(pyridin-2-yl)ethyl]propanamide
C18 H18 N4 O2
HWTVYWVFOWWESR-GFCCVEGCSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
C [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
5ME BindingDB:  4GV2 IC50: min: 6000, max: 1.00e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.188α = 90
b = 56.784β = 112.66
c = 56.618γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2013-10-16
    Changes: Database references