3C49

Human poly(ADP-ribose) polymerase 3, catalytic fragment in complex with an inhibitor KU0058948

• PDB DOI: https://doi.org/10.2210/pdb3C49/pdb

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


• Deposited: 2008-01-29 Released: 2008-02-12 
• Deposition Author(s): Lehtio, L., Karlberg, T., Arrowsmith, C.H., Berglund, H., Bountra, C., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Helleday, T., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Welin, M., Weigelt, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.257 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 

Starting Model: experimental

Literature

Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3.

Lehtio, L., Jemth, A.S., Collins, R., Loseva, O., Johansson, A., Markova, N., Hammarstrom, M., Flores, A., Holmberg-Schiavone, L., Weigelt, J., Helleday, T., Schuler, H., Karlberg, T.

(2009) J Med Chem 52: 3108-3111

• PubMed: 19354255 
• DOI: https://doi.org/10.1021/jm900052j
• Primary Citation of Related Structures:  
  3C49, 3C4H, 3CE0, 3FHB


• PubMed Abstract: 
  

  Poly(ADP-ribose) polymerases (PARPs) activate DNA repair mechanisms upon stress- and cytotoxin-induced DNA damage, and inhibition of PARP activity is a lead in cancer drug therapy. We present a structural and functional analysis of the PARP domain of human PARP-3 in complex with several inhibitors. Of these, KU0058948 is the strongest inhibitor of PARP-3 activity. The presented crystal structures highlight key features for potent inhibitor binding and suggest routes for creating isoenzyme-specific PARP inhibitors.

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Organizational Affiliation: 

Structural Genomics Consortium, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17177 Stockholm, 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: 40.13 kDa 
• Atom Count: 2,810 
• Modelled Residue Count: 357 
• 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, ADPRT3, ADPRTL3 EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6F1 (Homo sapiens) Go to UniProtKB:  Q9Y6F1
PHAROS:  Q9Y6F1 GTEx:  ENSG00000041880

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KU8	B [auth A]	4-[3-(1,4-diazepan-1-ylcarbonyl)-4-fluorobenzyl]phthalazin-1(2H)-one C21 H21 F N4 O2 HGEPGGJUGUMFHT-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KU8	PDBBind:  3C49	Kd: 70 (nM) from 1 assay(s)
	BindingDB:  3C49	Kd: 70 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.257 
• R-Value Work: 0.186 
• R-Value Observed: 0.191 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.79	α = 90
b = 57.19	β = 112.05
c = 56.47	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Lehtio, L., Karlberg, T., Arrowsmith, C.H., Berglund, H., Bountra, C., Busam, R., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Helleday, T., Herman, M.D., Johansson, A., Johansson, I., Kallas, A., Kotenyova, T., Moche, M., Nilsson, M.E., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Svensson, L., Thorsell, A.G., Tresaugues, L., Van den Berg, S., Welin, M., Weigelt, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description