6G4M

Torpedo californica acetylcholinesterase bound to uncharged hybrid reactivator 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structure-Based Optimization of Nonquaternary Reactivators of Acetylcholinesterase Inhibited by Organophosphorus Nerve Agents.

Santoni, G.de Sousa, J.de la Mora, E.Dias, J.Jean, L.Sussman, J.L.Silman, I.Renard, P.Y.Brown, R.C.D.Weik, M.Baati, R.Nachon, F.

(2018) J. Med. Chem. 61: 7630-7639

  • DOI: 10.1021/acs.jmedchem.8b00592
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Acetylcholinesterase (AChE), a key enzyme in the central and peripheral nervous systems, is the principal target of organophosphorus nerve agents. Quaternary oximes can regenerate AChE activity by displacing the phosphyl group of the nerve agent from ...

    Acetylcholinesterase (AChE), a key enzyme in the central and peripheral nervous systems, is the principal target of organophosphorus nerve agents. Quaternary oximes can regenerate AChE activity by displacing the phosphyl group of the nerve agent from the active site, but they are poorly distributed in the central nervous system. A promising reactivator based on tetrahydroacridine linked to a nonquaternary oxime is also an undesired submicromolar reversible inhibitor of AChE. X-ray structures and molecular docking indicate that structural modification of the tetrahydroacridine might decrease inhibition without affecting reactivation. The chlorinated derivative was synthesized and, in line with the prediction, displayed a 10-fold decrease in inhibition but no significant decrease in reactivation efficiency. X-ray structures with the derivative rationalize this outcome. We thus show that rational design based on structural studies permits the refinement of new-generation pyridine aldoxime reactivators that may be more effective in the treatment of nerve agent intoxication.


    Organizational Affiliation

    Université de Strasbourg, ICPEES, UMR CNRS 7515 , 67087 Strasbourg , France.,Department of Chemistry , University of Southampton , Highfield, Southampton , SO17 1BJ , United Kingdom.,Université Grenoble Alpes, CEA, CNRS, IBS , F-38000 Grenoble , France.,Department of Structural Biology , Weizmann Institute of Science , 76100 Rehovot , Israel.,Department of Neurobiology , Weizmann Institute of Science , 76100 Rehovot , Israel.,Département de Toxicologie et Risques Chimiques , Institut de Recherche Biomédicale des Armées , 91220 Brétigny-sur-Orge , France.,Université de Normandie, COBRA, UMR 6014, FR 3038, Université de Rouen, INSA de Rouen, CNRS , 76821 Mont-Saint-Aignan , France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acetylcholinesterase
A, B
537Tetronarce californicaMutation(s): 0 
Gene Names: ache
EC: 3.1.1.7
Find proteins for P04058 (Tetronarce californica)
Go to UniProtKB:  P04058
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
DQ5
Query on DQ5

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Download CCD File 
A, B
2-[(~{E})-hydroxyiminomethyl]-6-[4-(1,2,3,4-tetrahydroacridin-9-ylamino)butyl]pyridin-3-ol
C23 H26 N4 O2
WBLSVMZKFSZDDW-MFKUBSTISA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 91.276α = 90.00
b = 106.240β = 90.00
c = 150.456γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceReAChE

Revision History 

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references
  • Version 2.0: 2019-05-01
    Type: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary