Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.15 kDa 
• Atom Count: 2944 
• Modelled Residue Count: 353 
• Deposited Residue Count: 357 
• Unique protein chains: 1

4L7N

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

• PDB DOI: 10.2210/pdb4L7N/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-06-14 Released: 2014-02-19 
• Deposition Author(s): Karlberg, T., Thorsell, A.G., Lindgren, A.E.G., Ekblad, T., Spjut, S., Andersson, C.D., Weigelt, J., Linusson, A., Elofsson, M., Schuler, H.

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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 

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

• PubMed: 24188023 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 3	A	357	Homo sapiens	Mutation(s): 0  Gene Names: ADPRT3, ADPRTL3, PARP3 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1VB	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

Binding Affinity Annotations
ID	Source	Binding 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 = 54.945	α = 90
b = 56.822	β = 112.41
c = 56.427	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-14 
• Released Date: 2014-02-19 
Deposition Author(s): Karlberg, T., Thorsell, A.G., Lindgren, A.E.G., Ekblad, T., Spjut, S., Andersson, C.D., Weigelt, J., Linusson, A., Elofsson, M., Schuler, H.

Revision History  

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