7R0A

Structure of sarin phosphonylated acetylcholinesterase in complex with 2-((hydroxyimino)methyl)-1-(5-(4-methyl-3-nitrobenzamido)pentyl)pyridinium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acetylcholinesterase
A, B
543Mus musculusMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21836
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P21836-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
P15
Query on P15

Download Ideal Coordinates CCD File 
H [auth A]2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
C13 H28 O7
FHHGCKHKTAJLOM-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
L [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
I4H (Subject of Investigation/LOI)
Query on I4H

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
~{N}-ethyl-4-methyl-3-nitro-benzamide
C10 H12 N2 O3
NBDKJRNBTBHWNK-UHFFFAOYSA-N
TOE
Query on TOE

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B],
P [auth B]
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N
PG0
Query on PG0

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
I [auth A],
M [auth B],
N [auth B]
2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SGB
Query on SGB
A, B
L-PEPTIDE LINKINGC7 H16 N O5 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.848α = 90
b = 108.968β = 90
c = 227.813γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-27
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-27
    Changes: Database references
  • Version 1.3: 2024-01-31
    Changes: Data collection, Refinement description