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- PDB-9snd: Mus musculus acetylcholinesterase in complex with 2-(1H-indol-3-y... -

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Basic information

Entry
Database: PDB / ID: 9snd
TitleMus musculus acetylcholinesterase in complex with 2-(1H-indol-3-yl)-N-(2-methoxybenzyl)ethan-1-amine
ComponentsAcetylcholinesterase
KeywordsHYDROLASE / Reversible / inhibitor / insecticide
Function / homology
Function and homology information


serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane ...serine hydrolase activity / acetylcholine catabolic process / acetylcholinesterase / acetylcholine binding / osteoblast development / acetylcholine receptor signaling pathway / acetylcholinesterase activity / basement membrane / regulation of receptor recycling / side of membrane / collagen binding / laminin binding / neuromuscular junction / receptor internalization / positive regulation of cold-induced thermogenesis / retina development in camera-type eye / cell adhesion / synapse / perinuclear region of cytoplasm / cell surface / Golgi apparatus / protein homodimerization activity / extracellular space / 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-9YU / : / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL / Acetylcholinesterase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsEkstrom, F. / Forsgen, N.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council2017-00664 Sweden
CitationJournal: Rsc Med Chem / Year: 2025
Title: Potent and selective indole-based inhibitors targeting disease-transmitting mosquitoes.
Authors: Rajeshwari, R. / Duvauchelle, V. / Lindgren, C. / Stangner, K. / Knutsson, S. / Forsgren, N. / Ekstrom, F. / Kamau, L. / Linusson, A.
History
DepositionSep 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetylcholinesterase
B: Acetylcholinesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,79612
Polymers119,5292
Non-polymers2,26710
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.353, 111.104, 227.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Acetylcholinesterase / AChE


Mass: 59764.488 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, 263 molecules

#2: Chemical
ChemComp-A1JOW / 2-(1~{H}-indol-3-yl)-~{N}-[(2-methoxyphenyl)methyl]ethanamine


Mass: 280.364 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H20N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-9YU / 2-[2-[2-[2-[2-[2-(2-methoxyethoxy)ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanol


Mass: 340.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32O8
#4: 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
#5: Chemical ChemComp-TOE / 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL


Mass: 164.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 26-30 % PEG750 MME 0.1 M HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97996 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97996 Å / Relative weight: 1
ReflectionResolution: 2.4→29.68 Å / Num. obs: 168071 / % possible obs: 99.34 % / Redundancy: 3.5 % / Biso Wilson estimate: 48.63 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.08845 / Rpim(I) all: 0.05486 / Rrim(I) all: 0.1043 / Net I/σ(I): 7.78
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.8472 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 11817 / CC1/2: 0.823 / % possible all: 99.08

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→29.68 Å / SU ML: 0.2792 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.7596
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2226 1532 1.97 %
Rwork0.2088 76367 -
obs0.209 77899 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8336 0 163 253 8752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00228774
X-RAY DIFFRACTIONf_angle_d0.542811962
X-RAY DIFFRACTIONf_chiral_restr0.04171266
X-RAY DIFFRACTIONf_plane_restr0.00461562
X-RAY DIFFRACTIONf_dihedral_angle_d18.58073164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.2971150.30866866X-RAY DIFFRACTION99.08
2.48-2.570.31641410.2876818X-RAY DIFFRACTION98.91
2.57-2.670.2891600.27296813X-RAY DIFFRACTION98.87
2.67-2.790.31921350.26046873X-RAY DIFFRACTION99.14
2.79-2.940.27311350.25416848X-RAY DIFFRACTION99.32
2.94-3.120.27591560.25946854X-RAY DIFFRACTION99
3.12-3.360.22681260.23886941X-RAY DIFFRACTION99.65
3.36-3.70.23131440.21096963X-RAY DIFFRACTION99.52
3.7-4.230.18681350.18336995X-RAY DIFFRACTION99.87
4.23-5.330.16261390.16177083X-RAY DIFFRACTION99.9
5.33-29.680.20691460.18527313X-RAY DIFFRACTION99.45
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)
10.962521757640.42125499869-0.1746302838790.861890686152-0.4352122278631.88474424801-0.0380831807638-0.1149350321080.007984349730120.06841053308970.0343448703447-0.02381417775190.1090497888160.1087899168810.005552176045730.5740474637310.0274895152345-0.01843457518130.480642060250.02436530213450.45873246038533.920356412711.230344174723.8740660423
21.192863600550.224239166903-0.3395331980421.19827282569-0.6592712538473.10915971839-0.0108633475710.09517951200160.0259795524099-0.09712827533020.01177314548580.0740079593355-0.0777880455346-0.298321704242-0.03568237947590.475856746532-0.0251681082442-0.03161444682220.4968656527610.01276006030260.45592844286318.455319880415.84645954336.76918622879
34.031130944340.3871318577452.443162501417.46496359573-1.484565201524.92127831780.01933016846310.0153477232416-0.6384126144720.08126630714910.1986571114870.5656080015570.458531087461-1.24696519534-0.1622260940860.588601347638-0.193567894674-0.0143914378790.6723786007220.06696044383220.5995215310546.457056978651.2452456494914.141494448
43.43044819791-1.5332468089-3.12825947992.142530515682.51864380818.149001097560.1623330956790.0756348142881-0.171877933612-0.291117855558-0.09373854043420.08295877579190.04879171758980.0158400085457-0.02334899242330.665696271943-0.0665581736768-0.1163630502770.658847258008-0.02057589950320.54758612882917.29006953046.14304561684-1.14424617001
53.05279206554-0.385594647395-2.06492944931.253681467420.5483677916643.39807922937-0.09694873570330.3324997417470.127858892278-0.324407450498-0.08911564779820.216744147714-0.0909309793958-0.4203930891180.2191648788690.7622208291790.0505555342963-0.08114934419550.788471914135-0.1485574888920.581294395478-3.607179807576.37200086927-61.9546347237
60.631004009310.0343781667201-0.003902975703931.398760401520.205529427442.057468034490.1005363505420.257454340389-0.127238779993-0.204533180933-0.210361953350.160739387330.393358922425-0.3058239232890.07876461008710.648713576138-0.0094232074727-0.06636061740260.666938304887-0.1023974303840.4697582148211.521982721730.992728188184-51.7975674714
71.15753161294-0.5515221478820.01667023772011.397201067030.3582400006022.369916821930.1782573379640.197896082618-0.0387221125315-0.0794148201113-0.087600675397-0.124463473970.1874887180620.303873754041-0.08710863510490.5933746980430.0287057212167-0.03065736599110.632279706804-0.07156059004850.4561803647716.512287365.19856186372-46.6730834659
82.807025654950.4867023768990.4241637152913.1616999781-0.06274039523071.860513926030.438339847563-0.0919999082668-0.2081017714380.427173708808-0.202728998427-0.02399662270950.7891107015380.0645312941991-0.2732900624680.985344688067-0.0336075758617-0.07893635051620.5713154772450.009238235422040.49145313270213.610440064-6.24123679455-22.0055462619
91.220259556110.108217695030.04681052220462.13846047659-0.4369727167512.664997867580.152130734489-0.176864128575-0.02257821687540.245286101397-0.1823034565340.1713730429340.153452581711-0.354794222762-0.0009735659385670.58856866963-0.1038841793420.04815647514370.54679535935-0.1019471118580.4442128015410.4797850485225.90245166275-29.2706815833
100.7447453957860.008885643735091.0590159874.53536573679-0.8321347881075.625167683430.142859727425-0.4770070883360.340817338172-0.0478841368966-0.1591496537480.456782681448-0.225045621079-0.721946475211-0.02170458642290.7188040961910.03010782160170.01289114045230.713384224008-0.0787224819540.509627080385-1.3986633927122.434875165-28.9327926148
113.47888212669-0.05647362310181.750962664351.011390785890.2200660722912.869547294420.0514327498035-0.544188272194-0.1174865418120.2276366066380.0137402557771-0.04171509963580.1024427546290.333650720483-0.06517816174310.794745884945-0.0609056852824-0.01174655515820.623451935527-0.02451749950080.47052341543313.105655551311.346431492-21.6902158768
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 318 )AA1 - 3181 - 311
22chain 'A' and (resid 319 through 486 )AA319 - 486312 - 479
33chain 'A' and (resid 487 through 513 )AA487 - 513480 - 506
44chain 'A' and (resid 514 through 542 )AA514 - 542507 - 535
55chain 'B' and (resid 4 through 45 )BG4 - 451 - 42
66chain 'B' and (resid 46 through 142 )BG46 - 14243 - 139
77chain 'B' and (resid 143 through 331 )BG143 - 331140 - 321
88chain 'B' and (resid 332 through 382 )BG332 - 382322 - 372
99chain 'B' and (resid 383 through 486 )BG383 - 486373 - 476
1010chain 'B' and (resid 487 through 513 )BG487 - 513477 - 503
1111chain 'B' and (resid 514 through 543 )BG514 - 543504 - 533

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