5K5E | pdb_00005k5e

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

• PDB DOI: https://doi.org/10.2210/pdb5K5E/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2016-05-23 Released: 2016-07-27 
• Deposition Author(s): De la Mora, E., Dighe, S.N., Deora, G.S., Ross, B.P., Nachon, F., Brazzolotto, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

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

• PubMed: 27405689 
• DOI: https://doi.org/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 = 0.443 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 124.14 kDa 
• Atom Count: 8,862 
• Modelled Residue Count: 1,053 
• Deposited Residue Count: 1,058 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	529	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
Glycosylation
Glycosylation Sites: 5		Go to GlyGen: P06276-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6QS	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
NAG	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
GOL	U [auth B], V [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	K [auth A], S [auth B], T [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6QS	BindingDB:  5K5E	IC50: min: 443, max: 763 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.202 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.81	α = 90
b = 80.07	β = 90
c = 230.63	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): De la Mora, E., Dighe, S.N., Deora, G.S., Ross, B.P., Nachon, F., Brazzolotto, X.

Revision History  

• 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
• Version 2.1: 2023-02-15
  Changes: Database references, Structure summary
• Version 2.2: 2023-03-01
  Changes: Advisory
• Version 2.3: 2024-02-07
  Changes: Data collection, Refinement description
• Version 2.4: 2024-11-20
  Changes: Structure summary