5DYW

Crystal structure of human butyrylcholinesterase in complex with N-((1-benzylpiperidin-3-yl)methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide

PDB DOI: https://doi.org/10.2210/pdb5DYW/pdb

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

Deposited: 2015-09-25 Released: 2017-01-18
Deposition Author(s): Coquelle, N., Brus, B., Colletier, J.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.216
R-Value Work: 0.190
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 128.17 kDa
Atom Count: 9,234
Modelled Residue Count: 1,052
Deposited Residue Count: 1,060
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A, B	530	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06276
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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, E, G	2		N-Glycosylation	Interactions Focus chain C Focus chain E Focus chain G Interactions & Density Focus chain C Focus chain E Focus chain G
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D, F	3		N-Glycosylation	Interactions Focus chain D Focus chain F Interactions & Density Focus chain D Focus chain F
Glycosylation Resources
GlyTouCan: G21290RB GlyCosmos: G21290RB GlyGen: G21290RB

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, J, K	3		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain J Focus chain K Interactions & Density Focus chain H Focus chain I Focus chain J Focus chain K
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5HF Query on 5HF Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain AA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain AA [auth B]	AA [auth B], L [auth A]	N-{[(3S)-1-benzylpiperidin-3-yl]methyl}-N-(2-methoxyethyl)naphthalene-2-sulfonamide C₂₆ H₃₂ N₂ O₃ S NIHBOOKOQZGYSF-QHCPKHFHSA-N		Interactions Focus chain AA [auth B] Focus chain L [auth A] Interactions & Density Focus chain AA [auth B] Focus chain L [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain PA [auth B] SDF format, chain Z [auth A] SDF format, chain OA [auth B] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain OA [auth B]	LA [auth B] MA [auth B] NA [auth B] OA [auth B] PA [auth B] LA [auth B], MA [auth B], NA [auth B], OA [auth B], PA [auth B], Z [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain LA [auth B] Focus chain MA [auth B] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain Z [auth A]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A]	Y [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A]	BA [auth B] CA [auth B] DA [auth B] EA [auth B] FA [auth B] BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], M [auth A], N [auth A], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain IA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	GA [auth B] HA [auth B] IA [auth B] Q [auth A] R [auth A] GA [auth B], HA [auth B], IA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Interactions & Density Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain X [auth A] SDF format, chain JA [auth B] SDF format, chain W [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain W [auth A]	JA [auth B], KA [auth B], W [auth A], X [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth B] Focus chain KA [auth B] Focus chain W [auth A] Focus chain X [auth A] Interactions & Density Focus chain JA [auth B] Focus chain KA [auth B] Focus chain W [auth A] Focus chain X [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
5HF	BindingDB: 5DYW	IC50: 4.9 (nM) from 1 assay(s)
5HF	Binding MOAD: 5DYW	IC50: 4.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.216
R-Value Work: 0.190
R-Value Observed: 0.191
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.214	α = 90
b = 78.863	β = 90
c = 226.65	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Coquelle, N.

Brus, B.

Colletier, J.P.

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2020-03-25
Changes: Advisory, 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