4HEV

Clostridium Botulinum Serotype A Light Chain Inhibited By Adamantane Hydroxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Evaluation of adamantane hydroxamates as botulinum neurotoxin inhibitors: synthesis, crystallography, modeling, kinetic and cellular based studies.

Silhar, P.Silvaggi, N.R.Pellett, S.Johnson, E.A.Allen, K.N.Janda, K.D.

(2013) Bioorg.Med.Chem. 21: 1344-1348

  • DOI: 10.1016/j.bmc.2012.12.001

  • PubMed Abstract: 
  • Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opp ...

    Botulinum neurotoxins (BoNTs) are the most lethal biotoxins known to mankind and are responsible for the neuroparalytic disease botulism. Current treatments for botulinum poisoning are all protein based and thus have a limited window of treatment opportunity. Inhibition of the BoNT light chain protease (LC) has emerged as a therapeutic strategy for the treatment of botulism as it may provide an effective post exposure remedy. Using a combination of crystallographic and modeling studies a series of hydroxamates derived from 1-adamantylacetohydroxamic acid (3a) were prepared. From this group of compounds, an improved potency of about 17-fold was observed for two derivatives. Detailed mechanistic studies on these structures revealed a competitive inhibition model, with a K(i)=27 nM, which makes these compounds some of the most potent small molecule, non-peptidic BoNT/A LC inhibitors reported to date.


    Organizational Affiliation

    Department of Chemistry, and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Botulinum neurotoxin type A light chain
A, B
441Clostridium botulinumGene Names: botA (atx, bna)
EC: 3.4.24.69
Find proteins for P10845 (Clostridium botulinum)
Go to UniProtKB:  P10845
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
AXM
Query on AXM

Download SDF File 
Download CCD File 
A, B
N-hydroxy-2-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]acetamide
Adamantane acetic acid hydroxamate
C12 H19 N O2
JKZCKUGJZBWOQO-GOCCLTDMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AXMKi: 460 nM (99) BINDINGDB
AXMIC50: 1000 nM (99) BINDINGDB
AXMKi: 460 nM BINDINGMOAD
AXMKi: 460 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.601α = 90.00
b = 67.632β = 106.13
c = 99.408γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
PHASERphasing
HKL-2000data scaling
CBASSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-05-22
    Type: Database references