4L7N

Human artd3 (parp3) - catalytic domain in complex with inhibitor STO1542


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4L6Z, 4L70, 4L7L, 4L7N, 4L7O, 4L7P, 4L7R, 4L7U

  • 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 evaluation of 55 compounds in this class ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 3A357Homo sapiensMutation(s): 0 
Gene Names: ADPRT3ADPRTL3PARP3
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1VB
Query on 1VB

Download Ideal Coordinates CCD File 
B [auth A]3-(4-oxo-3,4-dihydroquinazolin-2-yl)-N-[(1S)-1-(4-sulfamoylphenyl)ethyl]propanamide
C19 H20 N4 O4 S
HHRFLQNTWASYFZ-LBPRGKRZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1VB BindingDB:  4L7N IC50: 1.44e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.945α = 90
b = 56.822β = 112.41
c = 56.427γ = 90
Software Package:
Software NamePurpose
GDAdata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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