7R02

Mus musculus acetylcholinesterase in complex with N-(3-(diethylamino)propyl)-4-methyl-3-nitrobenzamide

• PDB DOI: https://doi.org/10.2210/pdb7R02/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-02-01 Released: 2022-04-27 
• Deposition Author(s): Forsgren, N., Lindgren, C., Edvinsson, L., Linusson, A., Ekstrom, F.
• Funding Organization(s): Other government, Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.185 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 

Starting Model: experimental

Literature

Broad-Spectrum Antidote Discovery by Untangling the Reactivation Mechanism of Nerve-Agent-Inhibited Acetylcholinesterase.

Lindgren, C., Forsgren, N., Hoster, N., Akfur, C., Artursson, E., Edvinsson, L., Svensson, R., Worek, F., Ekstrom, F., Linusson, A.

(2022) Chemistry 28: e202200678-e202200678

• PubMed: 35420233 
• DOI: https://doi.org/10.1002/chem.202200678
• Primary Citation of Related Structures:  
  7QYN, 7R02, 7R0A, 7R2F, 7R3C, 7R4E


• PubMed Abstract: 
  

  Reactivators are vital for the treatment of organophosphorus nerve agent (OPNA) intoxication but new alternatives are needed due to their limited clinical applicability. The toxicity of OPNAs stems from covalent inhibition of the essential enzyme acetylcholinesterase (AChE), which reactivators relieve via a chemical reaction with the inactivated enzyme. Here, we present new strategies and tools for developing reactivators. We discover suitable inhibitor scaffolds by using an activity-independent competition assay to study non-covalent interactions with OPNA-AChEs and transform these inhibitors into broad-spectrum reactivators. Moreover, we identify determinants of reactivation efficiency by analysing reactivation and pre-reactivation kinetics together with structural data. Our results show that new OPNA reactivators can be discovered rationally by exploiting detailed knowledge of the reactivation mechanism of OPNA-inhibited AChE.

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Organizational Affiliation: 

Department of Chemistry, Umeå University, 901 87, Umeå, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 122.72 kDa 
• Atom Count: 9,026 
• Modelled Residue Count: 1,072 
• Deposited Residue Count: 1,086 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholinesterase	A, B	543	Mus musculus	Mutation(s): 0  Gene Names: Ache EC: 3.1.1.7
UniProt & NIH Common Fund Data Resources
Find proteins for P21836 (Mus musculus) Explore P21836  Go to UniProtKB:  P21836
IMPC:  MGI:87876
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P21836-1

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9YU	U [auth B]	2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol C15 H32 O8 AGWKUHGLWHMYTG-UHFFFAOYSA-N
I62 (Subject of Investigation/LOI)	C [auth A], L [auth B]	~{N}-[(~{E})-3-(diethylamino)prop-2-enyl]-4-methyl-3-nitro-benzamide C15 H22 N3 O3 GTWFMEPPTBDZDY-UXBLZVDNSA-O
NAG	D [auth A], E [auth A], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
PG0	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B]	2-(2-METHOXYETHOXY)ETHANOL C5 H12 O3 SBASXUCJHJRPEV-UHFFFAOYSA-N
EDO	K [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.185 
• R-Value Work: 0.169 
• R-Value Observed: 0.170 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.852	α = 90
b = 111.105	β = 90
c = 227.233	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Forsgren, N., Lindgren, C., Edvinsson, L., Linusson, A., Ekstrom, F.

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Funding Organization	Location	Grant Number
Other government	Sweden	--
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 2.0: 2022-06-15
  Changes: Database references, Non-polymer description
• Version 2.1: 2022-07-27
  Changes: Database references
• Version 2.2: 2024-01-31
  Changes: Data collection, Refinement description
• Version 2.3: 2024-10-23
  Changes: Structure summary