Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 79.15 kDa 
• Atom Count: 5817 
• Residue Count: 700 
• Unique protein chains: 1

1UK0

Crystal structure of catalytic domain of human poly(ADP-ribose) polymerase with a novel inhibitor

• DOI: 10.2210/pdb1UK0/pdb

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


• Deposited: 2003-08-13 Released: 2004-01-27 
• Deposition Author(s): Kinoshita, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 

Literature

Inhibitor-induced structural change of the active site of human poly(ADP-ribose) polymerase.

Kinoshita, T., Nakanishi, I., Warizaya, M., Iwashita, A., Kido, Y., Hattori, K., Fujii, T.

(2004) FEBS Lett 556: 43-46

• PubMed: 14706823 
• DOI: 10.1016/s0014-5793(03)01362-0
• Primary Citation of Related Structures:  
  1UK0


• PubMed Abstract: 
  

The crystal structure of human recombinant poly(ADP-ribose) polymerase (PARP) complexed with a potent inhibitor, FR257517, was solved at 3.0 A resolution. The fluorophenyl part of the inhibitor induces an amazing conformational change in the active site of PARP by motion of the side chain of the amino acid, Arg878, which forms the bottom of the active site. Consequently, a corn-shaped hydrophobic subsite, which consists of the side chains of Leu769, Ile879, Pro881, and the methylene chain of Arg878, newly emerges from the well-known active site.

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Organizational Affiliation: 

Exploratory Research Laboratories, Fujisawa Pharmaceutical Co. Ltd., 5-2-3, Tokodai, Tsukuba, 300-2698, Ibaraki, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase-1	A, B	350	Homo sapiens	Mutation(s): 0  Gene Names: PARP1, ADPRT, PPOL EC: 2.4.2.30 (PDB Primary Data), 2.4.2 (UniProt)
Find proteins for P09874 (Homo sapiens) Explore P09874  Go to UniProtKB:  P09874
NIH Common Fund Data Resources
PHAROS  P09874 GTEx  ENSG00000143799

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRM	A, B	2-{3-[4-(4-FLUOROPHENYL)-3,6-DIHYDRO-1(2H)-PYRIDINYL]PROPYL}-8-METHYL-4(3H)-QUINAZOLINONE C23 H24 F N3 O LOFDUAJQRUYHBR-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
FRM	IC50 :  8   nM  PDBBind
FRM	IC50:  8   nM  BindingDB
FRM	IC50:  16   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.246 
• R-Value Work: 0.219 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.82	α = 90
b = 53.55	β = 114.4
c = 92.01	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-08-13 
• Released Date: 2004-01-27 
Deposition Author(s): Kinoshita, T.

Revision History 

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance