Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 124.06 kDa 
• Atom Count: 8856 
• Modelled Residue Count: 1060 
• Deposited Residue Count: 1074 
• Unique protein chains: 1

6G4O

Non-aged form of Torpedo californica acetylcholinesterase inhibited by tabun analog NEDPA bound to uncharged reactivator 1

• DOI: 10.2210/pdb6G4O/pdb

• Classification: HYDROLASE
• Organism(s): Tetronarce californica
• Mutation(s): No 


• Deposited: 2018-03-28 Released: 2018-08-29 
• Deposition Author(s): Santoni, G., De la Mora, E., de Souza, J., Silman, I., Sussman, J., Baati, R., Weik, M., Nachon, F.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.264 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 

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

• PubMed: 30125110 
• DOI: 10.1021/acs.jmedchem.8b00592
• Primary Citation of 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.

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Organizational Affiliation: 

Département de Toxicologie et Risques Chimiques , Institut de Recherche Biomédicale des Armées , 91220 Brétigny-sur-Orge , France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	537	Tetronarce californica	Mutation(s): 0  Gene Names: ache EC: 3.1.1.7
UniProt
Find proteins for P04058 (Tetronarce californica) Explore P04058  Go to UniProtKB:  P04058

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DQ5 (Subject of Investigation/LOI)	F [auth A]	2-[(~{E})-hydroxyiminomethyl]-6-[4-(1,2,3,4-tetrahydroacridin-9-ylamino)butyl]pyridin-3-ol C23 H26 N4 O2 WBLSVMZKFSZDDW-MFKUBSTISA-N
P6G	U [auth B]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], M [auth B], N [auth B], P [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG4	I [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
ELT (Subject of Investigation/LOI)	E [auth A], O [auth B]	ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid C4 H12 N O3 P ZAMDBRIEKCKJBM-UHFFFAOYSA-N
CL	G [auth A], H [auth A], J [auth A], K [auth A], L [auth A], Q [auth B], S [auth B], T [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	R [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.78 Å
• R-Value Free: 0.264 
• R-Value Work: 0.187 
• R-Value Observed: 0.191 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.543	α = 90
b = 106.351	β = 90
c = 150.533	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-03-28 
• Released Date: 2018-08-29 
Deposition Author(s): Santoni, G., De la Mora, E., de Souza, J., Silman, I., Sussman, J., Baati, R., Weik, M., Nachon, F.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ReAChE

Revision History  

• Version 1.0: 2018-08-29
  Type: Initial release
  
• Version 1.1: 2018-09-26
  Changes: Data collection, Database references
• Version 2.0: 2019-05-01
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
• Version 2.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary