Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 143.43 kDa 
• Atom Count: 8979 
• Modelled Residue Count: 1053 
• Deposited Residue Count: 1204 
• Unique protein chains: 1

4TPK

Human butyrylcholinesterase in complex with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-N-(2-methoxyethyl)-2-naphthamide

• PDB DOI: 10.2210/pdb4TPK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2014-06-07 Released: 2014-10-22 
• Deposition Author(s): Coquelle, N., Brus, B., Colletier, J.P., Gobec, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Discovery, biological evaluation, and crystal structure of a novel nanomolar selective butyrylcholinesterase inhibitor.

Brus, B., Kosak, U., Turk, S., Pislar, A., Coquelle, N., Kos, J., Stojan, J., Colletier, J.P., Gobec, S.

(2014) J Med Chem 57: 8167-8179

• PubMed: 25226236 
• DOI: 10.1021/jm501195e
• Primary Citation of Related Structures:  
  4TPK


• PubMed Abstract: 
  

Butyrylcholinesterase (BChE) is regarded as a promising drug target as its levels and activity significantly increase in the late stages of Alzheimer's disease. To discover novel BChE inhibitors, we used a hierarchical virtual screening protocol followed by biochemical evaluation of 40 highest scoring hit compounds. Three of the compounds identified showed significant inhibitory activities against BChE. The most potent, compound 1 (IC50 = 21.3 nM), was resynthesized and resolved into its pure enantiomers. A high degree of stereoselective activity was revealed, and a dissociation constant of 2.7 nM was determined for the most potent stereoisomer (+)-1. The crystal structure of human BChE in complex with compound (+)-1 was solved, revealing the binding mode and providing clues for potential optimization. Additionally, compound 1 inhibited amyloid β(1-42) peptide self-induced aggregation into fibrils (by 61.7% at 10 μM) and protected cultured SH-SY5Y cells against amyloid-β-induced toxicity. These data suggest that compound 1 represents a promising candidate for hit-to-lead follow-up in the drug-discovery process against Alzheimer's disease.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	602	Homo sapiens	Mutation(s): 0  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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, J	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G61843VN GlyCosmos:  G61843VN GlyGen:  G61843VN

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N/A
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3F9	L [auth A], V [auth B]	N-{[(3R)-1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-carboxamide C29 H34 N2 O2 NRBCHFHGWACYAH-JOCHJYFZSA-N
NAG	K [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	M [auth A], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth B], N [auth A], O [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3F9	BindingDB:  4TPK	Ki: 2.7 (nM) from 1 assay(s)
		IC50: min: 13, max: 21 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.239 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.6	α = 90
b = 80.2	β = 90
c = 231.65	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-07 
• Released Date: 2014-10-22 
Deposition Author(s): Coquelle, N., Brus, B., Colletier, J.P., Gobec, S.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary