6G17 | pdb_00006g17

Non-aged form of Torpedo californica acetylcholinesterase inhibited by nerve agent tabun


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6G17

Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/acs.jmedchem.8b00592
  • Primary Citation Related Structures: 
    6FLD, 6FQN, 6G17, 6G4M, 6G4N, 6G4O, 6G4P

  • 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 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 Grenoble Alpes, CEA, CNRS, IBS , F-38000 Grenoble , France.

Macromolecule Content 

  • Total Structure Weight: 62.18 kDa 
  • Atom Count: 4,847 
  • Modeled Residue Count: 532 
  • Deposited Residue Count: 537 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholinesterase537Tetronarce californicaMutation(s): 0 
EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica)
Explore P04058 
Go to UniProtKB:  P04058
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04058
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PGE

Query on PGE



Download:Ideal Coordinates CCD File
F [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
NTJ

Query on NTJ



Download:Ideal Coordinates CCD File
B [auth A]R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE
C4 H12 N O2 P
VJBIKDDUGQICEU-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
E [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.214 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.767α = 90
b = 111.767β = 90
c = 137.215γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceReAChE

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2018-09-26
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-10-16
    Changes: Structure summary