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- PDB-9r3c: Recombinant human butyrylcholinesterase in complex with N-([(3S)-... -

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Basic information

Entry
Database: PDB / ID: 9r3c
TitleRecombinant human butyrylcholinesterase in complex with N-([(3S)-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
Chem-5HF / Cholinesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsBrazzolotto, X. / Kosak, 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)63,30214
Polymers59,7141
Non-polymers3,58913
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint7 kcal/mol
Surface area21460 Å2
Unit cell
Length a, b, c (Å)154.864, 154.864, 127.326
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

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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 , 3 types, 6 molecules

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


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-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

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Non-polymers , 5 types, 106 molecules

#5: 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
#6: Chemical ChemComp-5HF / N-{[(3S)-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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.2 Å3/Da / Density % sol: 61.52 %
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: BM07 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.31→49.18 Å / Num. obs: 33283 / % possible obs: 96.88 % / Redundancy: 7.4 % / Biso Wilson estimate: 57.36 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07456 / Rpim(I) all: 0.02866 / Rrim(I) all: 0.08024 / Net I/σ(I): 15.49
Reflection shellResolution: 2.31→2.393 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.759 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 3135 / CC1/2: 0.416 / Rpim(I) all: 0.6972 / Rrim(I) all: 1.901 / % possible all: 93.36

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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: 2.31→49.18 Å / SU ML: 0.3262 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6889
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2293 1652 5 %
Rwork0.19 31409 -
obs0.1919 33061 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.66 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 232 99 4534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00864602
X-RAY DIFFRACTIONf_angle_d0.96976261
X-RAY DIFFRACTIONf_chiral_restr0.0557695
X-RAY DIFFRACTIONf_plane_restr0.0074782
X-RAY DIFFRACTIONf_dihedral_angle_d10.3992695
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.380.3851300.33652450X-RAY DIFFRACTION92.67
2.38-2.450.34151400.2932609X-RAY DIFFRACTION97.83
2.45-2.540.26431320.27222637X-RAY DIFFRACTION98.72
2.54-2.640.34541400.26522625X-RAY DIFFRACTION98.68
2.64-2.760.33781220.27172606X-RAY DIFFRACTION97.25
2.76-2.910.30921470.24292635X-RAY DIFFRACTION98.55
2.91-3.090.28831330.22842644X-RAY DIFFRACTION98.16
3.09-3.330.26631360.2122634X-RAY DIFFRACTION97.4
3.33-3.670.2441400.18852606X-RAY DIFFRACTION97.27
3.67-4.20.21321570.15222629X-RAY DIFFRACTION97.07
4.2-5.290.16511360.1492642X-RAY DIFFRACTION95.89
5.29-49.180.18951390.16932692X-RAY DIFFRACTION93.52
Refinement TLS params.Method: refined / Origin x: 16.6900165263 Å / Origin y: 32.0042455676 Å / Origin z: 38.6255143394 Å
111213212223313233
T0.431183008028 Å2-0.051714902853 Å20.0630484194961 Å2-0.37108995864 Å20.0613256892785 Å2--0.468452676347 Å2
L1.55255058007 °20.364586362847 °2-0.506541251784 °2-1.78316838596 °2-0.261657063572 °2--2.02828172969 °2
S0.0052409602892 Å °0.0505028558917 Å °0.206990726793 Å °-0.180776932632 Å °0.0580274197978 Å °0.0206335265979 Å °-0.149126344897 Å °0.0946304120305 Å °-0.0641606353155 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 3 through 529 )

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