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- PDB-6fse: Mus musculus acetylcholinesterase in complex with 1-(4-(4-Ethylpi... -

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Basic information

Entry
Database: PDB / ID: 6fse
TitleMus musculus acetylcholinesterase in complex with 1-(4-(4-Ethylpiperazin-1-yl)piperidin-1-yl)-2-((4'-methoxy-[1,1'-biphenyl]-4-yl)oxy)ethanone dihydrochloride (15)
ComponentsAcetylcholinesterase
KeywordsPROTEIN BINDING / Inhibitor / hydrolase / acetylcholinesterase
Function / homology
Function and homology information


acetylcholine metabolic process / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / positive regulation of dendrite morphogenesis / cholinesterase activity / choline metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway ...acetylcholine metabolic process / serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / positive regulation of dendrite morphogenesis / cholinesterase activity / choline metabolic process / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / positive regulation of axonogenesis / basement membrane / regulation of receptor recycling / synaptic cleft / side of membrane / collagen binding / synapse assembly / laminin binding / neuromuscular junction / receptor internalization / response to insulin / nuclear envelope / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / presynaptic membrane / postsynaptic membrane / cell adhesion / membrane raft / endoplasmic reticulum lumen / hydrolase activity / axon / neuronal cell body / synapse / dendrite / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / 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 ...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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-1PG / Chem-E5K / DI(HYDROXYETHYL)ETHER / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsKnutsson, S. / Engdahl, C. / Kumari, R. / Kindahl, T. / Forsgren, N. / Lindgren, C. / Kitur, S. / Kamau, L. / Ekstrom, F. / Linusson, A.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2014-4218 Sweden
Swedish Research Council2014-2636 Sweden
CitationJournal: J.Med.Chem. / Year: 2018
Title: Noncovalent Inhibitors of Mosquito Acetylcholinesterase 1 with Resistance-Breaking Potency.
Authors: Knutsson, S. / Engdahl, C. / Kumari, R. / Forsgren, N. / Lindgren, C. / Kindahl, T. / Kitur, S. / Wachira, L. / Kamau, L. / Ekstrom, F. / Linusson, A.
History
DepositionFeb 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,9189
Polymers120,3242
Non-polymers1,5947
Water3,027168
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint12 kcal/mol
Surface area37510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.525, 111.885, 226.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 60161.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ache / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: P21836, acetylcholinesterase

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Non-polymers , 5 types, 175 molecules

#2: Chemical ChemComp-E5K / 1-[4-(4-ethylpiperazin-1-yl)piperidin-1-yl]-2-[4-(4-methoxyphenyl)phenoxy]ethanone


Mass: 437.574 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H35N3O3
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: PEG 750, Hepes buffer / PH range: 6.8-7.4

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Data collection

DiffractionMean temperature: 273.15 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.9184 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Nov 8, 2016
RadiationMonochromator: Rayonix SX-165 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→46.131 Å / Num. obs: 55911 / % possible obs: 99 % / Redundancy: 6.6 % / Biso Wilson estimate: 51.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0984 / Rrim(I) all: 0.107 / Net I/σ(I): 14.6
Reflection shellResolution: 2.7→2.796 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.6002 / Mean I/σ(I) obs: 3.13 / Num. unique obs: 5509 / CC1/2: 0.913 / Rrim(I) all: 0.651 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
SCALAdata scaling
Coot0.7.2 (4730)model building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1J06

1j06


Resolution: 2.7→46.131 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 1094 1.96 %
Rwork0.2036 --
obs0.2044 55910 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→46.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8332 0 96 169 8597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058697
X-RAY DIFFRACTIONf_angle_d0.60611872
X-RAY DIFFRACTIONf_dihedral_angle_d15.1095122
X-RAY DIFFRACTIONf_chiral_restr0.0451268
X-RAY DIFFRACTIONf_plane_restr0.0051554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.82290.37411320.27216756X-RAY DIFFRACTION99
2.8229-2.97170.34121360.26326730X-RAY DIFFRACTION99
2.9717-3.15780.27651460.24246775X-RAY DIFFRACTION99
3.1578-3.40160.30031260.23336818X-RAY DIFFRACTION100
3.4016-3.74380.22951410.20196788X-RAY DIFFRACTION99
3.7438-4.28520.2031350.17346888X-RAY DIFFRACTION100
4.2852-5.39750.18831350.17526913X-RAY DIFFRACTION99
5.3975-46.1380.23191430.1967148X-RAY DIFFRACTION99

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