4TVK | pdb_00004tvk

TORPEDO CALIFORNICA ACETYLCHOLINESTERASE IN COMPLEX WITH A CHLOROTACRINE-JUGLONE HYBRID INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4TVK

Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Multitarget Drug Design Strategy: Quinone-Tacrine Hybrids Designed To Block Amyloid-beta Aggregation and To Exert Anticholinesterase and Antioxidant Effects.

Nepovimova, E.Uliassi, E.Korabecny, J.Pena-Altamira, L.E.Samez, S.Pesaresi, A.Garcia, G.E.Bartolini, M.Andrisano, V.Bergamini, C.Fato, R.Lamba, D.Roberti, M.Kuca, K.Monti, B.Bolognesi, M.L.

(2014) J Med Chem 57: 8576-8589

  • DOI: https://doi.org/10.1021/jm5010804
  • Primary Citation Related Structures: 
    4TVK

  • PubMed Abstract: 

    We report the identification of multitarget anti-Alzheimer compounds designed by combining a naphthoquinone function and a tacrine fragment. In vitro, 15 compounds displayed excellent acetylcholinesterase (AChE) inhibitory potencies and interesting capabilities to block amyloid-β (Aβ) aggregation. The X-ray analysis of one of those compounds in complex with AChE allowed rationalizing the outstanding activity data (IC50 = 0.72 nM). Two of the compounds showed negligible toxicity in immortalized mouse cortical neurons Neuro2A and primary rat cerebellar granule neurons. However, only one of them was less hepatotoxic than tacrine in HepG2 cells. In T67 cells, both compounds showed antioxidant activity, following NQO1 induction. Furthermore, in Neuro2A, they were able to completely revert the decrease in viability induced by Aβ. Importantly, they crossed the blood-brain barrier, as demonstrated in ex vivo experiments with rats. When ex vivo results were combined with in vitro studies, these two compounds emerged to be promising multitarget lead candidates worthy of further pursuit.


  • Organizational Affiliation
    • Department of Pharmacy and Biotechnology, Alma Mater Studiorum-University of Bologna , Via Belmeloro 6, I-40126 Bologna, Italy.

Macromolecule Content 

  • Total Structure Weight: 61.76 kDa 
  • Atom Count: 4,627 
  • Modeled Residue Count: 534 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Acetylcholinesterase534Tetronarce 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
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TJH

Query on TJH



Download:Ideal Coordinates CCD File
E [auth A]2-({2-[(6-chloro-1,2,3,4-tetrahydroacridin-9-yl)amino]ethyl}amino)-5-hydroxynaphthalene-1,4-dione
C25 H22 Cl N3 O3
QOYHHKMVCBONOU-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.94α = 90
b = 111.94β = 90
c = 137.191γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata 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: 2014-10-08
    Type: Initial release
  • Version 1.1: 2014-11-05
    Changes: Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2023-12-20
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Structure summary