4GV2 | pdb_00004gv2

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

• PDB DOI: https://doi.org/10.2210/pdb4GV2/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-08-30 Released: 2013-06-19 
• 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: 
  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

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

• PubMed: 23742272 
• DOI: https://doi.org/10.1021/cb4002014
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Chemistry, Umeå University, Umeå, Sweden.

Biological Assembly 1  

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: 2,958 
• Modeled Residue Count: 354 
• Deposited Residue Count: 357 
• Unique protein chains: 1

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: 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5ME	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
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5ME	BindingDB:  4GV2	IC50: 1.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.194 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.188	α = 90
b = 56.784	β = 112.66
c = 56.618	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
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: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2013-10-16
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description