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 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


  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Poly [ADP-ribose] polymerase-1
A, B
350Homo sapiensMutation(s): 0 
Gene Names: PARP1 (ADPRT, PPOL)
EC: 2.4.2.30
Find proteins for P09874 (Homo sapiens)
Go to Gene View: PARP1
Go to UniProtKB:  P09874
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FRM
Query on FRM

Download SDF File 
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 - 16 nM (100) BINDINGDB
FRMIC50: 8 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.219 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 179.820α = 90.00
b = 53.550β = 114.40
c = 92.010γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance