6G1U | pdb_00006g1u

Crystal structure of Torpedo Californica acetylcholinesterase in complex with 9-Amino-6-chloro-1,2,3,4-tetrahydro-10-methylacridin-10-ium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 
    0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6G1U

Ligand Structure Quality Assessment 


This is version 2.3 of the entry. See complete history

Literature

Increasing Polarity in Tacrine and Huprine Derivatives: Potent Anticholinesterase Agents for the Treatment of Myasthenia Gravis.

Galdeano, C.Coquelle, N.Cieslikiewicz-Bouet, M.Bartolini, M.Perez, B.Clos, M.V.Silman, I.Jean, L.Colletier, J.P.Renard, P.Y.Munoz-Torrero, D.

(2018) Molecules 23

  • DOI: https://doi.org/10.3390/molecules23030634
  • Primary Citation Related Structures: 
    6G1U, 6G1V, 6G1W

  • PubMed Abstract: 

    Symptomatic treatment of myasthenia gravis is based on the use of peripherally-acting acetylcholinesterase (AChE) inhibitors that, in some cases, must be discontinued due to the occurrence of a number of side-effects. Thus, new AChE inhibitors are being developed and investigated for their potential use against this disease. Here, we have explored two alternative approaches to get access to peripherally-acting AChE inhibitors as new agents against myasthenia gravis, by structural modification of the brain permeable anti-Alzheimer AChE inhibitors tacrine, 6-chlorotacrine, and huprine Y. Both quaternization upon methylation of the quinoline nitrogen atom, and tethering of a triazole ring, with, in some cases, the additional incorporation of a polyphenol-like moiety, result in more polar compounds with higher inhibitory activity against human AChE (up to 190-fold) and butyrylcholinesterase (up to 40-fold) than pyridostigmine, the standard drug for symptomatic treatment of myasthenia gravis. The novel compounds are furthermore devoid of brain permeability, thereby emerging as interesting leads against myasthenia gravis.


  • Organizational Affiliation
    • Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, and Institute of Biomedicine (IBUB), University of Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain. cgaldeano@ub.edu.

Macromolecule Content 

  • Total Structure Weight: 131.91 kDa 
  • Atom Count: 9,962 
  • Modeled Residue Count: 1,063 
  • Deposited Residue Count: 1,130 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholinesterase
A, B
565Tetronarce 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: 3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E1K

Query on E1K



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth A]
U [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B]
6-chloranyl-10-methyl-1,2,3,4-tetrahydroacridin-10-ium-9-amine
C14 H16 Cl N2
NNLSQYGKFPZYHI-UHFFFAOYSA-O
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
C [auth A]
D [auth A]
E [auth A]
Q [auth B]
AA [auth B],
C [auth A],
D [auth A],
E [auth A],
Q [auth B],
R [auth B],
S [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
O [auth A]
P [auth A]
F [auth A],
G [auth A],
H [auth A],
O [auth A],
P [auth A],
T [auth B],
Z [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
Y [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.431α = 90
b = 106.6β = 90
c = 150.533γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-04
    Type: Initial release
  • 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
  • Version 2.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.3: 2024-11-13
    Changes: Structure summary