5NN0

Crystal structure of huBChE with N-((1-(2,3-dihydro-1H-inden-2-yl)piperidin-3-yl)methyl)-N-(2-(dimethylamino)ethyl)-2-naphthamide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The Magic of Crystal Structure-Based Inhibitor Optimization: Development of a Butyrylcholinesterase Inhibitor with Picomolar Affinity and in Vivo Activity.

Kosak, U.Brus, B.Knez, D.Zakelj, S.Trontelj, J.Pislar, A.Sink, R.Jukic, M.Zivin, M.Podkowa, A.Nachon, F.Brazzolotto, X.Stojan, J.Kos, J.Coquelle, N.Salat, K.Colletier, J.P.Gobec, S.

(2018) J. Med. Chem. 61: 119-139

  • DOI: 10.1021/acs.jmedchem.7b01086

  • PubMed Abstract: 
  • The enzymatic activity of butyrylcholinesterase (BChE) in the brain increases with the progression of Alzheimer's disease, thus classifying BChE as a promising drug target in advanced Alzheimer's disease. We used structure-based drug discovery approa ...

    The enzymatic activity of butyrylcholinesterase (BChE) in the brain increases with the progression of Alzheimer's disease, thus classifying BChE as a promising drug target in advanced Alzheimer's disease. We used structure-based drug discovery approaches to develop potent, selective, and reversible human BChE inhibitors. The most potent, compound 3, had a picomolar inhibition constant versus BChE due to strong cation-π interactions, as revealed by the solved crystal structure of its complex with human BChE. Additionally, compound 3 inhibits BChE ex vivo and is noncytotoxic. In vitro pharmacokinetic experiments show that compound 3 is highly protein bound, highly permeable, and metabolically stable. Finally, compound 3 crosses the blood-brain barrier, and it improves memory, cognitive functions, and learning abilities of mice in a scopolamine model of dementia. Compound 3 is thus a promising advanced lead compound for the development of drugs for alleviating symptoms of cholinergic hypofunction in patients with advanced Alzheimer's disease.


    Organizational Affiliation

    Institute of Pathological Physiology, Faculty of Medicine, University of Ljubljana , Vrazov trg 2, 1000 Ljubljana, Slovenia.,Institut de Recherche Biomédicale des Armées , 91223 Brétigny sur Orge, France.,Faculty of Pharmacy, Jagiellonian University , Medyczna 9 St., 30-688 Krakow, Poland.,Institute of Biochemistry, Faculty of Medicine, University of Ljubljana , Vrazov trg 2, 1000 Ljubljana, Slovenia.,Faculty of Pharmacy, University of Ljubljana , Aškerčeva 7, 1000 Ljubljana, Slovenia.,University Grenoble Alpes, and CNRS and CEA, IBS , F-38044 Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cholinesterase
A
529Homo sapiensMutation(s): 3 
Gene Names: BCHE (CHE1)
EC: 3.1.1.8
Find proteins for P06276 (Homo sapiens)
Go to Gene View: BCHE
Go to UniProtKB:  P06276
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PG
Query on 1PG

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A
2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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A
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
PEG
Query on PEG

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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
92H
Query on 92H

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A
~{N}-[[(3~{R})-1-(2,3-dihydro-1~{H}-inden-2-yl)piperidin-3-yl]methyl]-~{N}-[2-(dimethylamino)ethyl]naphthalene-2-carboxamide
C30 H37 N3 O
OFDHKZMZEXORRX-HSZRJFAPSA-N
 Ligand Interaction
MES
Query on MES

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Download CCD File 
A
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
92HIC50: 1.03 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.169 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 154.970α = 90.00
b = 154.970β = 90.00
c = 126.680γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release