D-(-)-Amygdalin   Click here for help

GtoPdb Ligand ID: 12451

Synonyms: amygdaloside | D-amygdalin | glucoprunasin | isoamygdalin
Compound class: Natural product or derivative
Comment: Amygdalin is a natural plant metabolite that can be isolated from Prunus mandshurica (Manchurian apricot) and Prunus davidiana (Chinese wild peach).
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Ligand Activity Visualisation Charts

These are box plot that provide a unique visualisation, summarising all the activity data for a ligand taken from ChEMBL and GtoPdb across multiple targets and species. Click on a plot to see the median, interquartile range, low and high data points. A value of zero indicates that no data are available. A separate chart is created for each target, and where possible the algorithm tries to merge ChEMBL and GtoPdb targets by matching them on name and UniProt accession, for each available species. However, please note that inconsistency in naming of targets may lead to data for the same target being reported across multiple charts.

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View interactive charts of activity data across species
2D Structure
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2D Structure

An image of the ligand's 2D structure. For small molecules with SMILES these are drawn using the NCI/CADD Chemical Identifier Resolver. Click on the image to access the chemical structure search tool with the ligand pre-loaded in the structure editor. For other types of ligands, e.g. longer nucleotides and peptides, a manually drawn representation of the molecule may be provided.

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Click here for structure editor
Physico-chemical Properties
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Physico-chemical Properties

Calculated molecular properties are available for small molecules and natural products (not peptides). Properties were generated using the CDK toolkit. All properties were selected to enable the prediction of the Lipinski Rule-of-Five profile or ‘druglikeness’ for each ligand. For more info on each category see the help pages.

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Hydrogen bond acceptors 12
Hydrogen bond donors 7
Rotatable bonds 7
Topological polar surface area 202.32
Molecular weight 457.43
XLogP -2.69
No. Lipinski's rules broken 2
SMILES / InChI / InChIKey
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SMILES / InChI / InChIKey

SMILES (Simplified Molecular Input Line Entry Specification) A specification for unambiguously describing the structure of chemical molecules using short ASCII strings. Canonical SMILES specify a unique representation of the 2D structure without chiral or isotopic specifications. Isomeric SMILES include chiral specification and isotopes.

Standard InChI (IUPAC International Chemical Identifier) and InChIKey InChI is a non-proprietary, standard, textual identifier for chemical substances designed to facilitate linking of information and database searching. An InChIKey is a simplified version of a full InChI, designed for easier web searching.

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Canonical SMILES C1=CC=C(C=C1)C(C#N)OC2C(C(C(C(COC3C(C(C(C(CO)O3)O)O)O)O2)O)O)O
Isomeric SMILES C1=CC=C(C=C1)C(C#N)OC2C(C(C(C(O2)COC3C(C(C(C(O3)CO)O)O)O)O)O)O
InChI InChI=1S/C20H27NO11/c21-6-10(9-4-2-1-3-5-9)30-20-18(28)16(26)14(24)12(32-20)8-29-19-17(27)15(25)13(23)11(7-22)31-19/h1-5,10-20,22-28H,7-8H2
InChI Key XUCIJNAGGSZNQT-UHFFFAOYSA-N
Classification Click here for help
Compound class Natural product or derivative
IUPAC Name Click here for help
2-phenyl-2-[3,4,5-trihydroxy-6-[[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxymethyl]oxan-2-yl]oxyacetonitrile
Synonyms Click here for help
amygdaloside | D-amygdalin | glucoprunasin | isoamygdalin
Database Links Click here for help
Specialist databases
GPCRdb Ligand D-(-)-Amygdalin
Other databases
ChEMBL Ligand CHEMBL1967951
GtoPdb PubChem SID 479821241
PubChem CID 2180
Search Google for chemical match using the InChIKey XUCIJNAGGSZNQT-UHFFFAOYSA-N
Search Google for chemicals with the same backbone XUCIJNAGGSZNQT
UniChem Compound Search for chemical match using the InChIKey XUCIJNAGGSZNQT-UHFFFAOYSA-N
UniChem Connectivity Search for chemical match using the InChIKey XUCIJNAGGSZNQT-UHFFFAOYSA-N