6SAM | pdb_00006sam

Structure of human butyrylcholinesterase in complex with 1-(2,3-dihydro-1H-inden2-yl)piperidin-3-yl N-phenyl carbamate

PDB DOI: https://doi.org/10.2210/pdb6SAM/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2019-07-17 Released: 2020-04-29
Deposition Author(s): Brazzolotto, X., Kosak, U., Strasek, N., Knez, D., Gobec, S., Nachon, F.
Funding Organization(s): French Ministry of Armed Forces

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.241 (Depositor), 0.247 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

N-alkylpiperidine carbamates as potential anti-Alzheimer's agents.

Kosak, U., Strasek, N., Knez, D., Jukic, M., Zakelj, S., Zahirovic, A., Pislar, A., Brazzolotto, X., Nachon, F., Kos, J., Gobec, S.

(2020) Eur J Med Chem 197: 112282-112282

PubMed: 32380361 Search on PubMed
DOI: https://doi.org/10.1016/j.ejmech.2020.112282
Primary Citation Related Structures:
6SAM

PubMed Abstract:
Compounds capable of interacting with single or multiple targets involved in Alzheimer's disease (AD) pathogenesis are potential anti-Alzheimer's agents. In our aim to develop new anti-Alzheimer's agents, a series of 36 new N-alkylpiperidine carbamates was designed, synthesized and evaluated for the inhibition of cholinesterases [acetylcholinesterase (AChE) and butyrylcholinesterase (BChE)] and monoamine oxidases [monoamine oxidase A (MAO-A and monoamine oxidase B (MAO-B)]. Four compounds are very promising: multiple AChE (IC ₅₀ = 7.31 μM), BChE (IC ₅₀ = 0.56 μM) and MAO-B (IC ₅₀ = 26.1 μM) inhibitor 10, dual AChE (IC ₅₀ = 2.25 μM) and BChE (IC ₅₀ = 0.81 μM) inhibitor 22, selective BChE (IC ₅₀ = 0.06 μM) inhibitor 13, and selective MAO-B (IC ₅₀ = 0.18 μM) inhibitor 16. Results of enzyme kinetics experiments showed that despite the carbamate group in the structure, compounds 10, 13, and 22 are reversible and non-time-dependent inhibitors of AChE and/or BChE. The resolved crystal structure of the complex of BChE with compound 13 confirmed the non-covalent mechanism of inhibition. Additionally, N-propargylpiperidine 16 is an irreversible and time-dependent inhibitor of MAO-B, while N-benzylpiperidine 10 is reversible. Additionally, compounds 10, 13, 16, and 22 should be able to cross the blood-brain barrier and are not cytotoxic to human neuronal-like SH-SY5Y and liver HepG2 cells. Finally, compounds 10 and 16 also prevent amyloid β _1-42 (Aβ _1-42)-induced neuronal cell death. The neuroprotective effects of compound 16 could be the result of its Aβ _1-42 anti-aggregation effects.

Organizational Affiliation

University of Ljubljana, Faculty of Pharmacy, Aškerčeva 7, 1000, Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 63.03 kDa
Atom Count: 4,521
Modeled Residue Count: 526
Deposited Residue Count: 529
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A	529	Homo sapiens	Mutation(s): 4 Gene Names: BCHE, CHE1 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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06276
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: P06276-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	3		N-Glycosylation	Interactions Focus chain B Focus chain C Focus chain D Interactions & Density Focus chain B Focus chain C Focus chain D
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L3H (Subject of Investigation/LOI) Query on L3H Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	[(3~{S})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-1-ium-3-yl] ~{N}-phenylcarbamate C₂₁ H₂₅ N₂ O₂ ISMYNYFEVMBAEI-FQEVSTJZSA-O		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	J [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A]	L [auth A], M [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain L [auth A] Focus chain M [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain I [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.241 (Depositor), 0.247 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.28	α = 90
b = 154.28	β = 90
c = 127.9	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-29

Deposition Author(s):

Funding Organization	Location	Grant Number
French Ministry of Armed Forces	France	NBC-4-C-4210

Revision History (Full details and data files)

Version 1.0: 2020-04-29
Type: Initial release
Version 1.1: 2020-05-20
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-20
Changes: Structure summary