1UK0

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • 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 s ...

    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.


    Organizational Affiliation

    Exploratory Research Laboratories, Fujisawa Pharmaceutical Co. Ltd., 5-2-3, Tokodai, Tsukuba, 300-2698, Ibaraki, Japan. takayoshi_kinoshita@po.fujisawa.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase-1AB350Homo sapiensMutation(s): 0 
Gene Names: PARP1ADPRTPPOL
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRM
Query on FRM

Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FRMIC50 :  8   nM  PDBBind
FRMIC50:  8   nM  BindingDB
FRMIC50:  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 = 179.82α = 90
b = 53.55β = 114.4
c = 92.01γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

View Full Validation Report



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