6G4O

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

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 

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Ligand Structure Quality Assessment 


This is version 2.1 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:  
    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 ...

    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: 

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



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AcetylcholinesteraseA, B537Tetronarce californicaMutation(s): 0 
Gene Names: ache
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DQ5
Query on DQ5
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
P6G
Query on P6G
Download Ideal Coordinates CCD File 
U [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N		 Ligand Interaction
NAG
Query on NAG
Download Ideal Coordinates CCD File 
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		 Ligand Interaction
PG4
Query on PG4
Download Ideal Coordinates CCD File 
I [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N		 Ligand Interaction
ELT
Query on ELT
Download Ideal Coordinates CCD File 
E [auth A],
O [auth B]		ethoxy-~{N},~{N}-dimethyl-phosphonamidic acid
C4 H12 N O3 P
ZAMDBRIEKCKJBM-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
J [auth A],
K [auth A],
L [auth A],
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		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
R [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
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 = 91.543α = 90
b = 106.351β = 90
c = 150.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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 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