4L70

Human artd3 (parp3) - catalytic domain in complex with inhibitor ME0352


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Chemical Probes to Study ADP-Ribosylation: Synthesis and Biochemical Evaluation of Inhibitors of the Human ADP-Ribosyltransferase ARTD3/PARP3.

Lindgren, A.E.Karlberg, T.Ekblad, T.Spjut, S.Thorsell, A.G.Andersson, C.D.Nhan, T.T.Hellsten, V.Weigelt, J.Linusson, A.Schuler, H.Elofsson, M.

(2013) J.Med.Chem. 56: 9556-9568

  • DOI: 10.1021/jm401394u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The racemic 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[1-(pyridin-2-yl)ethyl]propanamide, 1, has previously been identified as a potent but unselective inhibitor of diphtheria toxin-like ADP-ribosyltransferase 3 (ARTD3). Herein we describe synthesis and ...

    The racemic 3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[1-(pyridin-2-yl)ethyl]propanamide, 1, has previously been identified as a potent but unselective inhibitor of diphtheria toxin-like ADP-ribosyltransferase 3 (ARTD3). Herein we describe synthesis and evaluation of 55 compounds in this class. It was found that the stereochemistry is of great importance for both selectivity and potency and that substituents on the phenyl ring resulted in poor solubility. Certain variations at the meso position were tolerated and caused a large shift in the binding pose. Changes to the ethylene linker that connects the quinazolinone to the amide were also investigated but proved detrimental to binding. By combination of synthetic organic chemistry and structure-based design, two selective inhibitors of ARTD3 were discovered.


    Organizational Affiliation

    Department of Chemistry, Umeå University , SE-90187 Umeå, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase 3
A
357Homo sapiensMutation(s): 0 
Gene Names: PARP3 (ADPRT3, ADPRTL3)
EC: 2.4.2.30
Find proteins for Q9Y6F1 (Homo sapiens)
Go to Gene View: PARP3
Go to UniProtKB:  Q9Y6F1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1V9
Query on 1V9

Download SDF File 
Download CCD File 
A
3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[(1S)-1-phenylpropyl]propanamide
C20 H21 N3 O2
YAXDRRKYLDEMKO-INIZCTEOSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1V9IC50: 2200 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.061α = 90.00
b = 57.007β = 112.39
c = 56.686γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
GDAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-02-19
    Type: Initial release