Structure of PDB 5nap Chain A Binding Site BS01

Receptor Information
>5nap Chain A (length=532) Species: 7787 (Tetronarce californica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SELLVNTKSGKVMGTRVPVLSSHISAFLGIPFAEPPVGNMRFRRPEPKKP
WSGVWNASTYPNNCQQYVDEQFPGFSGSEMWNPNREMSEDCLYLNIWVPS
PRPKSTTVMVWIYGGGFYSGSSTLDVYNGKYLAYTEEVVLVSLSYRVGAF
GFLALHGSQEAPGNVGLLDQRMALQWVHDNIQFFGGDPKTVTIFGESAGG
ASVGMHILSPGSRDLFRRAILQSGSPNCPWASVSVAEGRRRAVELGRNLN
CNLNSDEELIHCLREKKPQELIDVEWNVLPFDSIFRFSFVPVIDGEFFPT
SLESMLNSGNFKKTQILLGVNKDEGSFFLLYGAPGFSKDSESKISREDFM
SGVKLSVPHANDLGLDAVTLQYTDWMDDNNGIKNRDGLDDIVGDHNVICP
LMHFVNKYTKFGNGTYLYFFNHRASNLVWPEWMGVIHGYEIEFVFGLPLV
KELNYTAEEEALSRRIMHYWATFAKTGNPNEPHSQESKWPLFTTKEQKFI
DLNTEPMKVHQRLRVQMCVFWNQFLPKLLNAT
Ligand information
Ligand IDDZ7
InChIInChI=1S/C24H27NO3/c1-27-22-14-19-13-20(24(26)21(19)15-23(22)28-2)12-17-8-10-25(11-9-17)16-18-6-4-3-5-7-18/h3-7,12,14-15,17H,8-11,13,16H2,1-2H3/b20-12+
InChIKeyLPMOTUSFDTTWJL-UDWIEESQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6COc1cc2c(cc1OC)C(=O)C(=CC3CCN(CC3)Cc4ccccc4)C2
CACTVS 3.385COc1cc2CC(=CC3CCN(CC3)Cc4ccccc4)C(=O)c2cc1OC
OpenEye OEToolkits 2.0.6COc1cc2c(cc1OC)C(=O)/C(=C/C3CCN(CC3)Cc4ccccc4)/C2
CACTVS 3.385COc1cc2CC(=C/C3CCN(CC3)Cc4ccccc4)\C(=O)c2cc1OC
FormulaC24 H27 N O3
Name(2~{E})-5,6-dimethoxy-2-[[1-(phenylmethyl)piperidin-4-yl]methylidene]-3~{H}-inden-1-one
ChEMBLCHEMBL168938
DrugBank
ZINCZINC000000597028
PDB chain5nap Chain A Residue 611 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nap Kinetic and structural studies on the interactions of Torpedo californica acetylcholinesterase with two donepezil-like rigid analogues.
Resolution2.17 Å
Binding residue
(original residue number in PDB)		Y70 W84 E199 W279 F330 F331 Y334
Binding residue
(residue number reindexed from 1)		Y67 W81 E196 W276 F327 F328 Y331
Annotation score1
Binding affinityMOAD: Ki=11.12nM
PDBbind-CN: -logKd/Ki=7.95,Kd=11.12nM
Enzymatic activity
Catalytic site (original residue number in PDB) G118 G119 G151 S200 A201 A239 F290 F292 E327 H440
Catalytic site (residue number reindexed from 1) G115 G116 G148 S197 A198 A236 F287 F289 E324 H437
Enzyme Commision number 3.1.1.7: acetylcholinesterase.
Gene Ontology
Molecular Function
GO:0003990 acetylcholinesterase activity
GO:0004104 cholinesterase activity
GO:0052689 carboxylic ester hydrolase activity
Biological Process
GO:0001507 acetylcholine catabolic process in synaptic cleft
GO:0006581 acetylcholine catabolic process
GO:0019695 choline metabolic process
Cellular Component
GO:0005615 extracellular space
GO:0005886 plasma membrane
GO:0043083 synaptic cleft
GO:0045202 synapse
GO:0098552 side of membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nap, PDBe:5nap, PDBj:5nap
PDBsum5nap
PubMed29651884
UniProtP04058|ACES_TETCF Acetylcholinesterase (Gene Name=ache)

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