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- PDB-9r9d: Recombinant human butyrylcholinesterase in complex with N-(2-meth... -

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Basic information

Entry
Database: PDB / ID: 9r9d
TitleRecombinant human butyrylcholinesterase in complex with N-(2-methoxyethyl)-N-{[1-(prop-2-yn-1-yl)pyrrolidin-3-yl]methyl}naphthalene-2-carboxamide
ComponentsCholinesterase
KeywordsHYDROLASE / Butyrylcholinesterase / inhibitor / complex
Function / homology
Function and homology information


cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process ...cholinesterase / : / neuroblast differentiation / response to folic acid / choline binding / Neurotransmitter clearance / cholinesterase activity / choline metabolic process / response to alkaloid / acetylcholine catabolic process / negative regulation of synaptic transmission / peptide hormone processing / hydrolase activity, acting on ester bonds / acetylcholinesterase activity / Aspirin ADME / Synthesis of PC / nuclear envelope lumen / catalytic activity / Synthesis, secretion, and deacylation of Ghrelin / xenobiotic metabolic process / response to glucocorticoid / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsBrazzolotto, X. / Kosak, U. / Nachon, F. / Gobec, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Ministry of Armed ForcesNBC-5-C-2316 France
CitationJournal: Chem.Biol.Interact. / Year: 2025
Title: N-Propargylpyrrolidine-based butyrylcholinesterase and monoamine oxidase inhibitors.
Authors: Kosak, U. / Knez, D. / Pislar, A. / Horvat, S. / Zakelj, S. / Igert, A. / Dias, J. / Nachon, F. / Brazzolotto, X. / Gobec, S.
History
DepositionMay 20, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,00513
Polymers59,7141
Non-polymers3,29212
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-4 kcal/mol
Surface area21370 Å2
Unit cell
Length a, b, c (Å)153.408, 153.408, 127.609
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.: 1
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.: 3
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.: 2 / 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 , 4 types, 216 molecules

#5: Chemical ChemComp-A1JDP / ~{N}-(2-methoxyethyl)-~{N}-[[(3~{R})-1-prop-2-ynylpyrrolidin-3-yl]methyl]naphthalene-2-carboxamide


Mass: 350.454 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H26N2O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
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: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 12, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 2.16→41.32 Å / Num. obs: 39490 / % possible obs: 95.46 % / Redundancy: 4.5 % / Biso Wilson estimate: 37.41 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1229 / Rpim(I) all: 0.06347 / Rrim(I) all: 0.1389 / Net I/σ(I): 8.77
Reflection shellResolution: 2.16→2.22 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8939 / Mean I/σ(I) obs: 1.46 / Num. unique obs: 2554 / CC1/2: 0.533 / Rpim(I) all: 0.4546 / Rrim(I) all: 1.007 / % possible all: 89.84

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.16→41.32 Å / SU ML: 0.1981 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.9038
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2138 1917 4.92 %
Rwork0.1774 37039 -
obs0.1791 38956 95.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.81 Å2
Refinement stepCycle: LAST / Resolution: 2.16→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4195 0 213 210 4618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724574
X-RAY DIFFRACTIONf_angle_d0.93166223
X-RAY DIFFRACTIONf_chiral_restr0.0553694
X-RAY DIFFRACTIONf_plane_restr0.0064781
X-RAY DIFFRACTIONf_dihedral_angle_d16.5481854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.220.2751100.25042471X-RAY DIFFRACTION89.84
2.22-2.280.31711400.25512399X-RAY DIFFRACTION88.84
2.28-2.340.27051640.2252661X-RAY DIFFRACTION97.85
2.34-2.420.23511510.20832655X-RAY DIFFRACTION97.46
2.42-2.510.23681310.19742678X-RAY DIFFRACTION97.67
2.51-2.610.23221220.2112683X-RAY DIFFRACTION97.63
2.61-2.720.27721240.2132703X-RAY DIFFRACTION97.42
2.72-2.870.25191420.20482670X-RAY DIFFRACTION97.13
2.87-3.050.20951390.19372665X-RAY DIFFRACTION96.72
3.05-3.280.22881450.18172659X-RAY DIFFRACTION96.26
3.28-3.610.211200.16972673X-RAY DIFFRACTION95.75
3.61-4.130.17741530.14072654X-RAY DIFFRACTION95.22
4.13-5.210.16291330.14012688X-RAY DIFFRACTION94.82
5.21-41.320.2131430.17232780X-RAY DIFFRACTION93.96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.415938856870.226276580285-0.4830611670941.53025544847-0.2313886861881.85820071036-0.07214661077240.2324919739430.0528281683313-0.3992810990220.08562034883-0.08460542993560.1200998181340.0362699603652-0.007254460463850.342989306722-0.03520012704940.03344390681420.2560277415440.04208410384010.25740187176218.773243953428.277910287427.4632928614
20.8987771513490.004922918096-0.1710468924211.21190901651-0.07475793237491.88244120366-0.03824317399580.1610746046880.437701725428-0.1193995674160.1465897713640.252967735586-0.458247610155-0.395070522009-0.08722642131630.3512710643710.01870186226-0.03645574471210.3648155794390.1240541642870.5016558734322.7372065511441.704084883431.6661650395
31.399217934430.283294198239-0.5969474331611.234501166330.03506417629491.391690594440.174488260981-0.4142201925990.2842601325220.2863960423380.04435705692710.0255958629413-0.4591911772140.232015477769-0.1987331027090.43441115733-0.06405810597340.09644103181660.404548984316-0.03119062601080.36582840445515.749933155344.449919406457.5032255192
41.022259647640.331343952082-0.4013479702612.044525294470.1330422004061.9622792978-0.00235658124406-0.22280143765-0.01057928682070.1048013396880.0178320468566-0.122768909230.1089300822470.241360722021-0.0148289541860.2310787333140.01587775749750.008883531616990.268879272820.05726243036970.23596489960321.293588673124.533568007950.3195194217
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 235 )4 - 2351 - 232
22chain 'A' and (resid 236 through 316 )236 - 316233 - 313
33chain 'A' and (resid 317 through 397 )317 - 397314 - 394
44chain 'A' and (resid 398 through 529 )398 - 529395 - 526

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