6F7Q | pdb_00006f7q

Human Butyrylcholinesterase complexed with N-Propargyliperidines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 3.0 of the entry. See complete history

Literature

Multi-target-directed ligands for treating Alzheimer's disease: Butyrylcholinesterase inhibitors displaying antioxidant and neuroprotective activities.

Knez, D.Coquelle, N.Pislar, A.Zakelj, S.Jukic, M.Sova, M.Mravljak, J.Nachon, F.Brazzolotto, X.Kos, J.Colletier, J.P.Gobec, S.

(2018) Eur J Med Chem 156: 598-617

  • DOI: https://doi.org/10.1016/j.ejmech.2018.07.033
  • Primary Citation Related Structures: 
    6F7Q

  • PubMed Abstract: 

    The limited clinical efficacy of current symptomatic treatment and minute effect on progression of Alzheimer's disease has shifted the research focus from single targets towards multi-target-directed ligands. Here, a potent selective inhibitor of human butyrylcholinesterase was used as the starting point to develop a new series of multifunctional ligands. A focused library of derivatives was designed and synthesised that showed both butyrylcholinesterase inhibition and good antioxidant activity as determined by the DPPH assay. The crystal structure of compound 11 in complex with butyrylcholinesterase revealed the molecular basis for its low nanomolar inhibition of butyrylcholinesterase (Ki = 1.09 ± 0.12 nM). In addition, compounds 8 and 11 show metal-chelating properties, and reduce the redox activity of chelated Cu 2+ ions in a Cu-ascorbate redox system. Compounds 8 and 11 decrease intracellular levels of reactive oxygen species, and are not substrates of the active efflux transport system, as determined in Caco2 cells. Compound 11 also protects neuroblastoma SH-SY5Y cells from toxic Aβ 1-42 species. These data indicate that compounds 8 and 11 are promising multifunctional lead ligands for treatment of Alzheimer's disease.


  • Organizational Affiliation
    • Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.

Macromolecule Content 

  • Total Structure Weight: 126.21 kDa 
  • Atom Count: 8,943 
  • Modeled Residue Count: 1,054 
  • Deposited Residue Count: 1,058 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholinesterase
A, B
529Homo sapiensMutation(s): 0 
Gene Names: BCHECHE1
EC: 3.1.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P06276 (Homo sapiens)
Explore P06276 
Go to UniProtKB:  P06276
PHAROS:  P06276
GTEx:  ENSG00000114200 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06276
Glycosylation
Glycosylation Sites: 5Go to GlyGen: P06276-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G61843VN
GlyCosmos: G61843VN
GlyGen: G61843VN
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G28454KX
GlyCosmos: G28454KX
GlyGen: G28454KX
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G21290RB
GlyCosmos: G21290RB
GlyGen: G21290RB

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CWQ

Query on CWQ



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
V [auth B],
W [auth B]
2-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-3-yl]methyl-(8-oxidanylquinolin-2-yl)carbonyl-amino]ethyl-dimethyl-azanium
C29 H37 N4 O2
JJYUCJIZTWRMMC-OAQYLSRUSA-O
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B],
Q [auth A],
R [auth A],
Z [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
BA [auth B],
CA [auth B],
S [auth A],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A],
M [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
N [auth A],
O [auth A],
P [auth A],
Y [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
X [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.248 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.14α = 90
b = 152.14β = 90
c = 141.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-05
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-05-01
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 3.0: 2025-10-01
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary