5K5E

Discovery and Structure-Activity Relationships of a Highly Selective Butyrylcholinesterase Inhibitor by Structure-Based Virtual Screening


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Discovery and Structure-Activity Relationships of a Highly Selective Butyrylcholinesterase Inhibitor by Structure-Based Virtual Screening.

Dighe, S.N.Deora, G.S.De la Mora, E.Nachon, F.Chan, S.Parat, M.O.Brazzolotto, X.Ross, B.P.

(2016) J Med Chem 59: 7683-7689

  • DOI: 10.1021/acs.jmedchem.6b00356
  • Primary Citation of Related Structures:  
    5K5E

  • PubMed Abstract: 
  • Structure-based virtual screening of two libraries containing 567 981 molecules was used to discover novel, selective BuChE inhibitors, which are potentially superior symptomatic treatments in late-stage Alzheimer's disease. Compound 16 was identified as a highly selective submicromolar inhibitor of BuChE (huBuChE IC50 = 0 ...

    Structure-based virtual screening of two libraries containing 567 981 molecules was used to discover novel, selective BuChE inhibitors, which are potentially superior symptomatic treatments in late-stage Alzheimer's disease. Compound 16 was identified as a highly selective submicromolar inhibitor of BuChE (huBuChE IC50 = 0.443 μM) with high permeability in the PAMPA-BBB model. The X-ray crystal structure of huBuChE in complex with 16 revealed the atomic-level interactions and offers opportunities for further development of the series.


    Organizational Affiliation

    School of Pharmacy, The University of Queensland , Brisbane, Queensland 4072, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CholinesteraseA, B529Homo sapiensMutation(s): 0 
Gene Names: BCHECHE1
EC: 3.1.1.8
Find proteins for P06276 (Homo sapiens)
Explore P06276 
Go to UniProtKB:  P06276
NIH Common Fund Data Resources
PHAROS:  P06276
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC, D, E2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6QS
Query on 6QS

Download Ideal Coordinates CCD File 
J [auth A], R [auth B][(2~{R})-oxolan-2-yl]methyl 4-(9-ethylcarbazol-3-yl)-2-methyl-5-oxidanylidene-4,6,7,8-tetrahydro-1~{H}-quinoline-3-carboxylate
C30 H32 N2 O4
SHBFRAVLHSPWTB-NGOKVRLYSA-N
 Ligand Interaction
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A] , G [auth A] , H [auth A] , I [auth A] , L [auth B] , M [auth B] , N [auth B] , O [auth B] , 
F [auth A],  G [auth A],  H [auth A],  I [auth A],  L [auth B],  M [auth B],  N [auth B],  O [auth B],  P [auth B],  Q [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
U [auth B], V [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
K [auth A], S [auth B], T [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.81α = 90
b = 80.07β = 90
c = 230.63γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2018-05-09
    Changes: Data collection, Source and taxonomy
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2019-10-02
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary