1UK1 | pdb_00001uk1

Crystal structure of human poly(ADP-ribose) polymerase complexed with a potent inhibitor

• PDB DOI: https://doi.org/10.2210/pdb1UK1/pdb

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


• Deposited: 2003-08-14 Released: 2004-09-14 
• Deposition Author(s): Kinoshita, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.274 (Depositor) 
• R-Value Work: 
  0.242 (Depositor), 0.280 (DCC) 
• R-Value Observed: 
  0.257 (Depositor) 

Literature

Rational approaches to discovery of orally active and brain-penetrable quinazolinone inhibitors of poly(ADP-ribose)polymerase

Hattori, K., Kido, Y., Yamamoto, H., Ishida, J., Kamijo, K., Murano, K., Ohkubo, M., Kinoshita, T., Iwashita, A., Mihara, K., Yamazaki, S., Matsuoka, N., Teramura, Y., Miyake, H.

(2004) J Med Chem 47: 4151-4154

• PubMed: 15293985 
• DOI: https://doi.org/10.1021/jm0499256
• Primary Citation of Related Structures:  
  1UK1


• PubMed Abstract: 
  

  A novel class of quinazolinone derivatives as potent poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors has been discovered. Key to success was application of a rational discovery strategy involving structure-based design, combinatorial chemistry, and classical SAR for improvement of potency and bioavailability. The new inhibitors were shown to bind to the nicotinamide-ribose binding site (NI site) and the adenosine-ribose binding site (AD site) of NAD+.

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Organizational Affiliation: 

Medicinal Chemistry Research Laboratories, Fujisawa Pharmaceutical Co., Ltd., 2-1-6 Kashima, Yodogawa-ku, Osaka 532-8514, Japan. kouji_hattori@ po.fujisawa.co.jp

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: 79.18 kDa 
• Atom Count: 5,757 
• 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
FRQ	C [auth A], D [auth B]	5-FLUORO-1-[4-(4-PHENYL-3,6-DIHYDROPYRIDIN-1(2H)-YL)BUTYL]QUINAZOLINE-2,4(1H,3H)-DIONE C23 H24 F N3 O2 PNPFDRCIGCUCMN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FRQ	BindingDB:  1UK1	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.274 (Depositor) 
• R-Value Work:  0.242 (Depositor), 0.280 (DCC) 
• R-Value Observed: 0.257 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.96	α = 90
b = 53.27	β = 113.8
c = 91.47	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: 2004-09-14 
Deposition Author(s): Kinoshita, T.

Revision History  

• Version 1.0: 2004-09-14
  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