9QPU | pdb_00009qpu

Structure of human butyrylcholinesterase inhibited by the Ellman's reaction product, 2-[(3-carboxy-4-nitrophenyl)disulfanyl]ethyl-trimethylazanium

PDB DOI: https://doi.org/10.2210/pdb9QPU/pdb

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

Deposited: 2025-03-29 Released: 2025-11-19
Deposition Author(s): Brazzolotto, X., Stojan, J.
Funding Organization(s): French Ministry of Armed Forces

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.238 (Depositor), 0.237 (DCC)
R-Value Work:
0.183 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The product of Ellman's reaction inhibits cholinesterases.

Stojan, J., Brazzolotto, X.

(2025) Protein Sci 34: e70371-e70371

PubMed: 41229096 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.70371
Primary Citation Related Structures:
9QPU

PubMed Abstract:
Kinetic and crystallographic studies reveal that the binding of the thiocholine-thionitrobenzoic acid product, released during the measurement of thioester-analog substrates hydrolysis according to Ellman's method, inhibits cholinesterases by a pure competitive mechanism. This can only be recorded as the progressive accumulation of the product upon subsequent additions of substrate aliquots. A wide affinity variation was observed among several tested enzymes, with the highest values found in human butyrylcholinesterase and Torpedo acetylcholinesterase. Nearly two orders of magnitude lower affinities were determined with human, mouse, and electrophorus acetylcholinesterases, and human atypical butyrylcholinesterase. These findings can be explained by the unexpected accommodation of the thiocholine-thionitrobenzoic acid in the active site of human butyrylcholinesterase, with the positively charged trimethylammonium choline pointing to the enzyme's peripheral site. At the same time, the carboxyl group of the nitrobenzoic moiety interacts with the enzyme's oxyanion hole. This explains the virtual absence of product inhibition in atypical human butyrylcholinesterase (D70G), purified or in plasma.

Organizational Affiliation

Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.

Macromolecule Content

Total Structure Weight: 64.45 kDa
Atom Count: 4,663
Modeled Residue Count: 527
Deposited Residue Count: 529
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cholinesterase	A	529	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06276
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain A	Go to GlyGen: P06276-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

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

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1I9A (Subject of Investigation/LOI) Query on A1I9A Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth A]	H [auth A], L [auth A]	2-[(3-carboxy-4-nitro-phenyl)disulfanyl]ethyl-trimethyl-azanium C₁₂ H₁₇ N₂ O₄ S₂ HRJGWYMNBPLENY-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain L [auth A] Interactions & Density Focus chain H [auth A] Focus chain L [auth A]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A]	F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
ETM (Subject of Investigation/LOI) Query on ETM Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain N [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain N [auth A]	I [auth A], K [auth A], N [auth A]	2-(TRIMETHYLAMMONIUM)ETHYL THIOL C₅ H₁₄ N S VFUGTBZQGUVGEX-UHFFFAOYSA-O		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain N [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A]	Q [auth A] R [auth A] S [auth A] T [auth A] U [auth A] Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions 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] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density 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] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	J [auth A], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain J [auth A] Focus chain O [auth A] Focus chain P [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain M [auth A] MOL2 format, chain M [auth A] mmCIF format, chain M [auth A]	M [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Interactions & Density Focus chain M [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain Z [auth A]	Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain Z [auth A] Interactions & Density Focus chain Z [auth A]