Record Information
Version1.0
Creation date2010-04-08 22:10:49 UTC
Update date2019-11-26 03:08:45 UTC
Primary IDFDB013636
Secondary Accession NumbersNot Available
Chemical Information
FooDB NameAmygdalin
DescriptionAmygdalin, also known as (R)-amygdaloside or (R)-laenitrile, belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. Amygdalin is an extremely weak basic (essentially neutral) compound (based on its pKa). Amygdalin is found, on average, in the highest concentration within a few different foods, such as apricots, peachs, and european plums and in a lower concentration in apples and quinces. Amygdalin has also been detected, but not quantified in, several different foods, such as fruits, sour cherries, passion fruits, loquats, and almonds. This could make amygdalin a potential biomarker for the consumption of these foods.
CAS Number29883-15-6
Structure
Thumb
Synonyms
SynonymSource
(-)-D-Mandelonitrile beta-D-gentiobiosideHMDB
(R)-AmygdalinHMDB
(R)-AmygdalosideHMDB
(R)-LaenitrileHMDB
AmygdalosideHMDB
D(-)-Mandelonitrile-beta-D-gentiobiosideHMDB
D(-)-Mandelonitrile-β-D-gentiobiosideHMDB
D-AmygdalinHMDB
D-Mandelonitrile-beta-D-glucosido-6-beta-D-glucosideHMDB
GlucoprunasinHMDB
Mandelonitrile gentiobiosideHMDB
Mandelonitrile-β-gentiobiosideHMDB
NSC 15780HMDB
Mandelonitrile-beta-gentiobiosideHMDB
NeoamygdalinHMDB
LaetrileHMDB
Mandelonitrile beta gentiobiosideHMDB
AmygdalinMeSH
(-)-d-mandelonitrile beta-d-gentiobiosidebiospider
(r)-amygdalinbiospider
(r)-amygdalosidebiospider
(r)-laenitrilebiospider
D-amygdalinbiospider
D-mandelonitrile-beta-D-glucosido-6-beta-D-glucosidebiospider
D(-)-mandelonitrile-β-d-gentiobiosidebiospider
D(-)-mandelonitrile-beta-d-gentiobiosidebiospider
Mandelonitrile-β-gentiobiosidebiospider
Predicted Properties
PropertyValueSource
Water Solubility35.3 g/LALOGPS
logP-1.3ALOGPS
logP-2.6ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)11.91ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area202.32 ŲChemAxon
Rotatable Bond Count7ChemAxon
Refractivity102.51 m³·mol⁻¹ChemAxon
Polarizability44.61 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Chemical FormulaC20H27NO11
IUPAC name2-phenyl-2-{[3,4,5-trihydroxy-6-({[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}methyl)oxan-2-yl]oxy}acetonitrile
InChI IdentifierInChI=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 KeyXUCIJNAGGSZNQT-UHFFFAOYSA-N
Isomeric SMILESOCC1OC(OCC2OC(OC(C#N)C3=CC=CC=C3)C(O)C(O)C2O)C(O)C(O)C1O
Average Molecular Weight457.4285
Monoisotopic Molecular Weight457.158410711
Classification
Description Belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentCyanogenic glycosides
Alternative Parents
Substituents
  • Cyanogenic glycoside
  • Disaccharide
  • O-glycosyl compound
  • Monocyclic benzene moiety
  • Oxane
  • Benzenoid
  • Secondary alcohol
  • Polyol
  • Nitrile
  • Carbonitrile
  • Acetal
  • Organoheterocyclic compound
  • Oxacycle
  • Primary alcohol
  • Alcohol
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic nitrogen compound
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External Descriptors
Ontology
Disposition

Route of exposure:

Source:

Biological location:

Role

Industrial application:

Biological role:

Physico-Chemical Properties - Experimental
Physico-Chemical Properties - Experimental
PropertyValueReference
Physical stateSolid
Physical DescriptionNot Available
Mass CompositionC 52.51%; H 5.95%; N 3.06%; O 38.47%DFC
Melting PointMp 214°DFC
Boiling PointNot Available
Experimental Water SolubilityNot Available
Experimental logPNot Available
Experimental pKaNot Available
Isoelectric pointNot Available
ChargeNot Available
Optical Rotation[a]25D -40.6 (H2O)DFC
Spectroscopic UV DataNot Available
DensityNot Available
Refractive IndexNot Available
Spectra
Spectra
EI-MS/GC-MS
TypeDescriptionSplash KeyView
Predicted GC-MSAmygdalin, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positivesplash10-00mx-3964600000-28e032c9faa617e24d81Spectrum
Predicted GC-MSAmygdalin, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positivesplash10-0aor-3851049000-e90b077fb54d8ae5064fSpectrum
MS/MS
TypeDescriptionSplash KeyView
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0910500000-43b5416a1c65aade6dd7Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00lr-0900000000-a7b743b4f6c48ceeeec3Spectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-2900000000-c994efea7d35cfc3bc8dSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a59-1920600000-bca6d39107a0a3d2c07fSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-001i-2900100000-3b83f13850f0c4b209beSpectrum
Predicted MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-003r-6900000000-d6216be611d875daf695Spectrum
NMRNot Available
ChemSpider ID2095
ChEMBL IDNot Available
KEGG Compound IDC08325
Pubchem Compound ID2180
Pubchem Substance IDNot Available
ChEBI ID27613
Phenol-Explorer IDNot Available
DrugBank IDNot Available
HMDB IDHMDB35030
CRC / DFC (Dictionary of Food Compounds) IDJDX91-A:JFR77-K
EAFUS IDNot Available
Dr. Duke IDAMYGDALIN
BIGG IDNot Available
KNApSAcK IDC00001437
HET IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
Flavornet IDNot Available
GoodScent IDNot Available
SuperScent IDNot Available
Wikipedia IDAmygdalin
Phenol-Explorer Metabolite IDNot Available
Duplicate IDSNot Available
Old DFC IDSNot Available
Associated Foods
FoodContent Range AverageReference
FoodReference
Biological Effects and Interactions
Health Effects / Bioactivities
DescriptorIDDefinitionReference
anti inflammatory35472 A substance that reduces or suppresses inflammation.DUKE
anti spasmodic52217 Any substance introduced into a living organism with therapeutic or diagnostic purpose.DUKE
anti tussive52217 Any substance introduced into a living organism with therapeutic or diagnostic purpose.DUKE
bitterDUKE
cancer preventive35610 A substance that inhibits or prevents the proliferation of neoplasms.DUKE
cyanogenicDUKE
expectorant52217 Any substance introduced into a living organism with therapeutic or diagnostic purpose.DUKE
toxic52209 A role played by the molecular entity or part thereof which causes the development of a pathological process.DUKE
EnzymesNot Available
PathwaysNot Available
MetabolismNot Available
BiosynthesisNot Available
Organoleptic Properties
FlavoursNot Available
Files
MSDSNot Available
References
Synthesis ReferenceNot Available
General ReferenceNot Available
Content Reference— Duke, James. 'Dr. Duke's Phytochemical and Ethnobotanical Databases. United States Department of Agriculture.' Agricultural Research Service, Accessed April 27 (2004).
— Shinbo, Y., et al. 'KNApSAcK: a comprehensive species-metabolite relationship database.' Plant Metabolomics. Springer Berlin Heidelberg, 2006. 165-181.