1UK0 | pdb_00001uk0

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

• PDB DOI: https://doi.org/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 (Depositor) 
• R-Value Work: 
  0.219 (Depositor), 0.210 (DCC) 

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: https://doi.org/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]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 79.15 kDa 
• Atom Count: 5,817 
• Modeled Residue Count: 700 
• Deposited Residue Count: 700 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FRM	C [auth A], D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
FRM	BindingDB:  1UK0	IC50: min: 8, max: 16 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.219 (Depositor), 0.210 (DCC) 

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

• 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
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations