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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 66.64 kDa 
• Atom Count: 4533 
• Modelled Residue Count: 526 
• Deposited Residue Count: 557 
• Unique protein chains: 1

6QAB

Human Butyrylcholinesterase in complex with (S)-N-(1-((2-cycloheptylethyl)amino)-3-(1H-indol-3-yl)-1-oxopropan-2-yl)-N,N-dimethylbutan-1-aminium

• PDB DOI: 10.2210/pdb6QAB/pdb

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


• Deposited: 2018-12-19 Released: 2019-03-27 
• Deposition Author(s): Brazzolotto, X., Nachon, F., Harst, M., Knez, D., Gobec, S.
• Funding Organization(s): French Ministry of Armed Forces

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

Tryptophan-derived butyrylcholinesterase inhibitors as promising leads against Alzheimer's disease.

Meden, A., Knez, D., Jukic, M., Brazzolotto, X., Grsic, M., Pislar, A., Zahirovic, A., Kos, J., Nachon, F., Svete, J., Gobec, S., Groselj, U.

(2019) Chem Commun (Camb) 55: 3765-3768

• PubMed: 30864579 
• DOI: 10.1039/c9cc01330j
• Primary Citation of Related Structures:  
  6QAA, 6QAB, 6QAC, 6QAD, 6QAE


• PubMed Abstract: 
  

We have identified tryptophan-based selective nanomolar butyrylcholinesterase (BChE) inhibitors. They are defined according to their chemical modularity, novel binding mode revealed by five solved crystal structures with human BChE, low cytotoxicity, and predicted permeability of the blood-brain barrier. Altogether, these factors indicate their potential as unique lead compounds for symptomatic therapy against Alzheimer's disease.

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Organizational Affiliation: 

Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A	557	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

Oligosaccharides

Help

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

Entity ID: 3
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	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HUQ (Subject of Investigation/LOI)	N [auth A]	butyl-[(2~{S})-1-(2-cycloheptylethylamino)-3-(1~{H}-indol-3-yl)-1-oxidanylidene-propan-2-yl]-dimethyl-azanium C26 H42 N3 O KYGLOTKSZWORPK-VWLOTQADSA-O
NAG	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	M [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	O [auth A], P [auth A], Q [auth A], R [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	H [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
HUQ	Binding MOAD:  6QAB	IC50: 6.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.49 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.632	α = 90
b = 153.632	β = 90
c = 128.589	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-12-19 
• Released Date: 2019-03-27 
Deposition Author(s): Brazzolotto, X., Nachon, F., Harst, M., Knez, D., Gobec, S.

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Funding Organization	Location	Grant Number
French Ministry of Armed Forces	France	PDH-2-NRBC-3-C-3201

Revision History  

• Version 1.0: 2019-03-27
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary