5LKR | pdb_00005lkr

Human Butyrylcholinesterase complexed with N-Propargyliperidines


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 
    0.238 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.185 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5LKR

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

N-Propargylpiperidines with naphthalene-2-carboxamide or naphthalene-2-sulfonamide moieties: Potential multifunctional anti-Alzheimer's agents.

Kosak, U.Knez, D.Coquelle, N.Brus, B.Pislar, A.Nachon, F.Brazzolotto, X.Kos, J.Colletier, J.P.Gobec, S.

(2017) Bioorg Med Chem 25: 633-645

  • DOI: https://doi.org/10.1016/j.bmc.2016.11.032
  • Primary Citation Related Structures: 
    5LKR

  • PubMed Abstract: 

    In the brains of patients with Alzheimer's disease, the enzymatic activities of butyrylcholinesterase (BChE) and monoamine oxidase B (MAO-B) are increased. While BChE is a viable therapeutic target for alleviation of symptoms caused by cholinergic hypofunction, MAO-B is a potential therapeutic target for prevention of neurodegeneration in Alzheimer's disease. Starting with piperidine-based selective human (h)BChE inhibitors and propargylamine-based MAO inhibitors, we have designed, synthesized and biochemically evaluated a series of N-propargylpiperidines. All of these compounds inhibited hBChE with good selectivity over the related enzyme, acetylcholinesterase, and crossed the blood-brain barrier in a parallel artificial membrane permeation assay. The crystal structure of one of the inhibitors (compound 3) in complex with hBChE revealed its binding mode. Three compounds (4, 5, 6) showed concomitant inhibition of MAO-B. Additionally, the most potent hBChE inhibitor 7 and dual BChE and MAO-B inhibitor 6 were non-cytotoxic and protected neuronal SH-SY5Y cells from toxic amyloid β-peptide species.


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

Macromolecule Content 

  • Total Structure Weight: 136.63 kDa 
  • Atom Count: 8,751 
  • Modeled Residue Count: 1,053 
  • Deposited Residue Count: 1,148 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cholinesterase
A, B
574Homo 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: 7Go to GlyGen: P06276-1
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
C, D, F, G, H
C, D, F, G, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
E
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G86851RC
GlyCosmos: G86851RC
GlyGen: G86851RC
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
J
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G61843VN
GlyCosmos: G61843VN
GlyGen: G61843VN

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6YC

Query on 6YC



Download:Ideal Coordinates CCD File
N [auth A],
W [auth B]
~{N}-(2-methoxyethyl)-~{N}-[[(3~{S})-1-prop-2-ynylpiperidin-3-yl]methyl]naphthalene-2-carboxamide
C23 H28 N2 O2
FTXYXGOUTSVXAQ-IBGZPJMESA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
K [auth A]
Q [auth B]
R [auth B]
S [auth B]
T [auth B]
K [auth A],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
X [auth B],
Y [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
FUL

Query on FUL



Download:Ideal Coordinates CCD File
L [auth A]beta-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
P [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
M [auth A],
O [auth A],
V [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6YC BindingDB:  5LKR IC50: 3306 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free:  0.238 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.185 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.681α = 90
b = 79.463β = 90
c = 228.869γ = 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: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-01-11
    Changes: Database references
  • Version 1.2: 2017-08-16
    Changes: Advisory, Data collection
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary