4L6S

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

• PDB DOI: https://doi.org/10.2210/pdb4L6S/pdb

• Classification: transferase/transferase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-06-12 Released: 2013-08-07 
• Deposition Author(s): Dougan, D.R., Mol, C.D., Lawson, J.D.

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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 

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

• PubMed: 23850199 
• 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.

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Organizational Affiliation: 

Takeda California, 10410 Science Center Dr, San Diego, CA 92121, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.73 kDa 
• Atom Count: 5,891 
• Modelled Residue Count: 703 
• Deposited Residue Count: 706 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly [ADP-ribose] polymerase 1	A, B	353	Homo sapiens	Mutation(s): 1  Gene Names: ADPRT, PARP 1, PARP1, PPOL 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
1WQ	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
ID	Source	Binding Affinity
1WQ	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 = 48.525	α = 90
b = 93.045	β = 90
c = 165.193	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Dougan, D.R., Mol, C.D., Lawson, J.D.

Revision History  

• 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