9QPU | pdb_00009qpu

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


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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Literature

The product of Ellman's reaction inhibits cholinesterases.

Stojan, J.Brazzolotto, X.

(2025) Protein Sci 34: e70371-e70371

  • DOI: https://doi.org/10.1002/pro.70371
  • Primary Citation of 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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholinesterase529Homo sapiensMutation(s): 4 
Gene Names: BCHECHE1
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06276
Glycosylation
Glycosylation Sites: 6Go to GlyGen: P06276-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC
GlyCosmos:  G86851RC
GlyGen:  G86851RC
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D 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
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I9A (Subject of Investigation/LOI)
Query on A1I9A

Download Ideal Coordinates CCD File 
H [auth A],
L [auth A]
2-[(3-carboxy-4-nitro-phenyl)disulfanyl]ethyl-trimethyl-azanium
C12 H17 N2 O4 S2
HRJGWYMNBPLENY-UHFFFAOYSA-O
NAG
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ETM (Subject of Investigation/LOI)
Query on ETM

Download Ideal Coordinates CCD File 
I [auth A],
K [auth A],
N [auth A]
2-(TRIMETHYLAMMONIUM)ETHYL THIOL
C5 H14 N S
VFUGTBZQGUVGEX-UHFFFAOYSA-O
SO4
Query on SO4

Download Ideal Coordinates CCD File 
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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A],
O [auth A],
P [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA
Query on NA

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Z [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • 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) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.062α = 90
b = 155.062β = 90
c = 127.645γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
autoPROCdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French Ministry of Armed ForcesFranceNBC-5-C-2316

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-19
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Database references