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- PDB-9r3b: Recombinant human Butyrylcholinesterase in complex with N-([(3R)-... -

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Basic information

Entry
Database: PDB / ID: 9r3b
TitleRecombinant human Butyrylcholinesterase in complex with N-([(3R)-1-benzylpiperidin-3-yl]methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / inhibitor / complex
Function / homology
Function and homology information


cholinesterase / cocaine metabolic process / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / response to alkaloid / cholinesterase activity / choline metabolic process / negative regulation of synaptic transmission ...cholinesterase / cocaine metabolic process / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / response to alkaloid / cholinesterase activity / choline metabolic process / negative regulation of synaptic transmission / acetylcholine catabolic process / hydrolase activity, acting on ester bonds / peptide hormone processing / acetylcholinesterase activity / nuclear envelope lumen / Synthesis of PC / Aspirin ADME / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / response to glucocorticoid / xenobiotic metabolic process / learning / amyloid-beta binding / blood microparticle / endoplasmic reticulum lumen / negative regulation of cell population proliferation / enzyme binding / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Acetylcholinesterase, tetramerisation domain / Acetylcholinesterase tetramerisation domain / : / Cholinesterase / Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / N-acetyl-alpha-neuraminic acid / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBrazzolotto, X. / Kosac, U. / Gobec, S. / Nachon, F.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-2316 France
CitationJournal: Chem.Biol.Interact. / Year: 2025
Title: Chiral switch of a butyrylcholinesterase inhibitor for the treatment of Alzheimer's disease
Authors: Kosak, U. / Knez, D. / Benetik, S.F. / Sokolov, P.M. / Pislar, A. / Horvat, S. / Stojan, J. / Lv, B. / Zhang, W. / Wang, Y. / Wang, Q. / Igert, A. / Dias, J. / Nachon, F. / Brazzolotto, X. / Sun, H. / Gobec, S.
History
DepositionMay 3, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,02018
Polymers59,7141
Non-polymers4,30717
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint16 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.808, 154.808, 128.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-896-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cholinesterase / Acylcholine acylhydrolase / Butyrylcholine esterase / Choline esterase II / Pseudocholinesterase


Mass: 59713.512 Da / Num. of mol.: 1
Mutation: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide)
Source method: isolated from a genetically manipulated source
Details: N17Q, N455Q, N481Q, N486Q mutations compared to mature wild type sequence to avoid too much N-glycozylation. Numeration on the maturated enzyme (devoid of the signal peptide)
Source: (gene. exp.) Homo sapiens (human) / Gene: BCHE, CHE1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P06276, cholinesterase

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Sugars , 4 types, 7 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 207 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-A1JC3 / N-(2-methoxyethyl)-N-[[(3R)-1-(phenylmethyl)piperidin-3-yl]methyl]naphthalene-2-sulfonamide / N-([(3R)-1-benzylpiperidin-3-yl]methyl)-N-(2-methoxyethyl)naphthalene-2-sulfonamide


Mass: 452.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H32N2O3S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.22 Å3/Da / Density % sol: 61.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.15→48.95 Å / Num. obs: 42480 / % possible obs: 99.84 % / Redundancy: 8.9 % / Biso Wilson estimate: 47.84 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1071 / Rpim(I) all: 0.03738 / Rrim(I) all: 0.1139 / Net I/σ(I): 12.77
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 1.934 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 4151 / CC1/2: 0.506 / Rpim(I) all: 0.6357 / Rrim(I) all: 2.042

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→48.95 Å / SU ML: 0.2516 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.9537
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2208 2134 5.03 %
Rwork0.1809 40327 -
obs0.1829 42461 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.44 Å2
Refinement stepCycle: LAST / Resolution: 2.15→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 278 197 4670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874616
X-RAY DIFFRACTIONf_angle_d0.90716276
X-RAY DIFFRACTIONf_chiral_restr0.0544703
X-RAY DIFFRACTIONf_plane_restr0.0072778
X-RAY DIFFRACTIONf_dihedral_angle_d11.2161698
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.26971150.27432643X-RAY DIFFRACTION99.64
2.2-2.260.34521310.29192646X-RAY DIFFRACTION99.71
2.26-2.320.28181380.25742668X-RAY DIFFRACTION100
2.32-2.380.27311390.23652670X-RAY DIFFRACTION100
2.38-2.460.28191380.22782659X-RAY DIFFRACTION100
2.46-2.550.28771350.22152673X-RAY DIFFRACTION99.93
2.55-2.650.2831720.2222624X-RAY DIFFRACTION99.96
2.65-2.770.23931430.20942679X-RAY DIFFRACTION100
2.77-2.920.25751510.19752665X-RAY DIFFRACTION100
2.92-3.10.23091440.19582689X-RAY DIFFRACTION100
3.1-3.340.23291480.19612689X-RAY DIFFRACTION100
3.34-3.680.17811550.17092680X-RAY DIFFRACTION99.79
3.68-4.210.20521620.15112700X-RAY DIFFRACTION99.86
4.21-5.30.1871160.13732772X-RAY DIFFRACTION99.55
5.3-48.950.20361470.17442870X-RAY DIFFRACTION99.64
Refinement TLS params.Method: refined / Origin x: 16.7896112269 Å / Origin y: 32.0649626991 Å / Origin z: 39.106158542 Å
111213212223313233
T0.350356110521 Å2-0.0216010690912 Å20.0345965368036 Å2-0.333181424751 Å20.0347488905194 Å2--0.358139484649 Å2
L0.932685685181 °20.336894959938 °2-0.29493637574 °2-0.929165454574 °2-0.17136838405 °2--1.04121425943 °2
S-0.0156107661893 Å °-0.0174600889532 Å °0.0926051157543 Å °-0.0914986561491 Å °0.0578682496759 Å °0.0196622297044 Å °0.00518070463511 Å °0.0237792553003 Å °-3.52715100824E-7 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 4 through 529 )

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