4L6S

PARP complexed with benzo[1,4]oxazin-3-one inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Discovery of novel benzo[b][1,4]oxazin-3(4H)-ones as poly(ADP-ribose)polymerase inhibitors

Gangloff, A.R.Brown, J.de Jong, R.Dougan, D.R.Grimshaw, C.E.Hixon, M.Jennings, A.Kamran, R.Kiryanov, A.O'Connell, S.Taylor, E.Vu, P.

(2013) Bioorg Med Chem Lett 23: 4501-4505

  • DOI: https://doi.org/10.1016/j.bmcl.2013.06.055
  • Primary Citation of Related Structures:  
    4L6S

  • PubMed Abstract: 

    Structure based drug design of a series of novel 1,4-benzoxazin-3-one derived PARP-1 inhibitors are described. The synthesis, enzymatic & cellular activities and pharmacodynamic effects are described. Optimized analogs demonstrated inhibition of poly-ADP-ribosylation in SW620 tumor bearing nude mice through 24h following a single dose.


  • Organizational Affiliation

    Takeda California, 10410 Science Center Dr, San Diego, CA 92121, USA. anthony.gangloff@takeda.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly [ADP-ribose] polymerase 1
A, B
353Homo sapiensMutation(s): 1 
Gene Names: ADPRTPARP 1PARP1PPOL
EC: 2.4.2.30
UniProt & NIH Common Fund Data Resources
Find proteins for P09874 (Homo sapiens)
Explore P09874 
Go to UniProtKB:  P09874
PHAROS:  P09874
GTEx:  ENSG00000143799 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09874
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1WQ
Query on 1WQ

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
(2S)-6-{[4-(4-chlorophenyl)-3,6-dihydropyridin-1(2H)-yl]methyl}-2-methyl-2H-1,4-benzoxazin-3(4H)-one
C21 H21 Cl N2 O2
UXKGKMDPTXLNNA-AWEZNQCLSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1WQ Binding MOAD:  4L6S Kd: 3 (nM) from 1 assay(s)
BindingDB:  4L6S Kd: 3 (nM) from 1 assay(s)
PDBBind:  4L6S IC50: 3 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.525α = 90
b = 93.045β = 90
c = 165.193γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-07
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations