Structure of PDB 5yc8 Chain A Binding Site BS01

Receptor Information
>5yc8 Chain A (length=384) Species: 562,9606 [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPYKTFEVVFIVLVAGSLSLVTIIGNILVMVSIKVNRHLQTVNNYFLFSL
ACADLIIGVFSMNLYTLYTVIGYWPLGPVVCDLWLALDYVVSNARVMNLL
IISFDRYFCVTKPLTYPVKRTTKMAGMMIAAAWVLSFILWAPAILFWQFI
VGVRTVEDGECYIQFFSNAAVTFGTAIAAFYLPVIIMTVLYWHISRASKA
DLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDK
SPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAY
IQKYLSREKKVTRTILAILLAFIITWAPYNVMVLINTFCAPCIPNTVWTI
GYWLCYINSTINPACYALCNATFKKTFKHLLMCH
Ligand information
Ligand ID3C0
InChIInChI=1S/C18H24NO4/c1-19(2)14-8-12(9-15(19)17-16(14)23-17)22-18(21)13(10-20)11-6-4-3-5-7-11/h3-7,12-17,20H,8-10H2,1-2H3/q+1/t12-,13-,14-,15+,16-,17+/m1/s1
InChIKeyLZCOQTDXKCNBEE-IKIFYQGPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C[N+]1(C2CC(CC1C3C2O3)OC(=O)C(CO)c4ccccc4)C
OpenEye OEToolkits 1.9.2C[N+]1([C@@H]2CC(C[C@H]1[C@H]3[C@@H]2O3)OC(=O)[C@H](CO)c4ccccc4)C
CACTVS 3.385C[N+]1(C)[CH]2CC(C[CH]1[CH]3O[CH]23)OC(=O)[CH](CO)c4ccccc4
CACTVS 3.385C[N+]1(C)[C@@H]2CC(C[C@H]1[C@@H]3O[C@H]23)OC(=O)[C@H](CO)c4ccccc4
ACDLabs 12.01O=C(OC1CC2[N+](C(C1)C3OC23)(C)C)C(c4ccccc4)CO
FormulaC18 H24 N O4
NameN-methyl scopolamine;
(1R,2R,4S,5S,7s)-7-{[(2S)-3-hydroxy-2-phenylpropanoyl]oxy}-9,9-dimethyl-3-oxa-9-azoniatricyclo[3.3.1.0~2,4~]nonane
ChEMBLCHEMBL376897
DrugBankDB11315
ZINCZINC000100047524
PDB chain5yc8 Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5yc8 Structural insights into the subtype-selective antagonist binding to the M2muscarinic receptor
Resolution2.5 Å
Binding residue
(original residue number in PDB)		D103 Y104 S107 N108 W155 A191 A194 W400 Y403 N404 Y426 C429
Binding residue
(residue number reindexed from 1)		D88 Y89 S92 N93 W140 A176 A179 W326 Y329 N330 Y352 C355
Annotation score1
Binding affinityMOAD: Kd=6.4nM
PDBbind-CN: -logKd/Ki=8.19,Kd=6.4nM
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0004930 G protein-coupled receptor activity
GO:0005506 iron ion binding
GO:0009055 electron transfer activity
GO:0016907 G protein-coupled acetylcholine receptor activity
GO:0020037 heme binding
GO:0046872 metal ion binding
Biological Process
GO:0007186 G protein-coupled receptor signaling pathway
GO:0022900 electron transport chain
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0042597 periplasmic space

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yc8, PDBe:5yc8, PDBj:5yc8
PDBsum5yc8
PubMed30420692
UniProtP08172|ACM2_HUMAN Muscarinic acetylcholine receptor M2 (Gene Name=CHRM2);
P0ABE7|C562_ECOLX Soluble cytochrome b562 (Gene Name=cybC)

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