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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:27:18 UTC
Update Date2021-10-13 06:34:41 UTC
HMDB IDHMDB0033699
Secondary Accession Numbers
  • HMDB33699
Metabolite Identification
Common NameLinamarin
DescriptionLinamarin, also known as phaseolunatin, belongs to the class of organic compounds known as cyanogenic glycosides. These are glycosides in which the aglycone moiety contains a cyanide group. Linamarin exists in all living organisms, ranging from bacteria to humans. In humans, linamarin is involved in the lansoprazole metabolism pathway. Linamarin is a bitter tasting compound. Linamarin has been detected, but not quantified in, several different foods, such as spirulinas (Spirulina), celeriacs (Apium graveolens var. rapaceum), chinese cinnamons (Cinnamomum aromaticum), green beans (Phaseolus vulgaris), and tronchuda cabbages (Brassica oleracea var. costata). This could make linamarin a potential biomarker for the consumption of these foods. Linamarin is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review a significant number of articles have been published on Linamarin.
Structure
Data?1563862446
Synonyms
ValueSource
1-Cyano-1-methylethyl beta-D-glucosideChEBI
PhaseolunatinChEBI
1-Cyano-1-methylethyl b-D-glucosideGenerator
1-Cyano-1-methylethyl β-D-glucosideGenerator
2-(b-D-Glucopyranosyloxy)-2-methylpropanenitrile, 9ciHMDB
2-(beta-D-Glucopyranosyloxy)-2-methyl-propanenitrileHMDB
2-(beta-D-Glucopyranosyloxy)-2-methylpropanenitrileHMDB
alpha-Hydroxyisobutyronitrile-beta-D-glucoseHMDB
ManihotoxinHMDB
Chemical FormulaC10H17NO6
Average Molecular Weight247.2451
Monoisotopic Molecular Weight247.105587281
IUPAC Name2-methyl-2-{[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}propanenitrile
Traditional Namelinamarin
CAS Registry Number554-35-8
SMILES
[H][C@]1(O)[C@]([H])(O)[C@@]([H])(CO)O[C@@]([H])(OC(C)(C)C#N)[C@]1([H])O
InChI Identifier
InChI=1S/C10H17NO6/c1-10(2,4-11)17-9-8(15)7(14)6(13)5(3-12)16-9/h5-9,12-15H,3H2,1-2H3/t5-,6-,7+,8-,9+/m1/s1
InChI KeyQLTCHMYAEJEXBT-ZEBDFXRSSA-N
Chemical Taxonomy
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
  • Hexose monosaccharide
  • O-glycosyl compound
  • Monosaccharide
  • Oxane
  • Secondary alcohol
  • Polyol
  • Organoheterocyclic compound
  • Oxacycle
  • Nitrile
  • Carbonitrile
  • Acetal
  • Primary alcohol
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organic nitrogen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
  • beta-D-glucoside (CHEBI:16441 )
  • Cyanogenic glucosides derived from valine or isoleucine (C01594 )
Ontology
Disposition

Biological location

Source

Route of exposure

Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point143 - 144 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility564900 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Spectral PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility66.8 g/LALOGPS
logP10(-1.2) g/LALOGPS
logP10(-1.8) g/LChemAxon
logS10(-0.57) g/LALOGPS
pKa (Strongest Acidic)12.21ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area123.17 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity54.95 m³·mol⁻¹ChemAxon
Polarizability23.34 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Spectral Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+157.25731661259
DarkChem[M-H]-150.52431661259

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Linamarin,1TMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]1O1851.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]1O1867.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H](O)[C@H]1O1889.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O[Si](C)(C)C1845.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]1O1903.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O1883.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1879.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]1O1881.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#5CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C1872.3Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TMS,#6CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H](O)[C@H]1O[Si](C)(C)C1859.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O1929.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1922.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1899.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C1915.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,4TMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C)[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)[C@H]1O[Si](C)(C)C1946.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TBDMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O2098.5Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TBDMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O2117.1Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TBDMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](O)[C@H]1O2123.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,1TBDMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C2094.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O2372.9Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O2345.4Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2347.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O2360.8Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#5CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C2341.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,2TBDMS,#6CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C2352.6Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TBDMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O2559.7Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TBDMS,#2CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2562.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TBDMS,#3CC(C)(C#N)O[C@@H]1O[C@H](CO)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2542.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,3TBDMS,#4CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)[C@H]1O[Si](C)(C)C(C)(C)C2551.0Semi standard non polarhttps://arxiv.org/abs/1905.12712
Linamarin,4TBDMS,#1CC(C)(C#N)O[C@@H]1O[C@H](CO[Si](C)(C)C(C)(C)C)[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)[C@H]1O[Si](C)(C)C(C)(C)C2763.2Semi standard non polarhttps://arxiv.org/abs/1905.12712
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Linamarin GC-MS (Non-derivatized) - 70eV, Positivesplash10-0bu0-9530000000-e58b8985888c18c2b6442017-07-27Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Linamarin GC-MS (4 TMS) - 70eV, Positivesplash10-00di-3121490000-6e31a29cb4593bc0a0f12017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Linamarin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Linamarin GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , negative-QTOFsplash10-014i-0940000000-bf243e2c29ff6b26fcf22017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , negative-QTOFsplash10-014i-0950000000-79243dda9f61101991c62017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , positive-QTOFsplash10-0udi-0910000000-1f3450a50f0470bcbca42017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , positive-QTOFsplash10-0udi-0910000000-a1faa4a6e57a8ab982592017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , positive-QTOFsplash10-0006-0390000000-dbccc3f4d1e4a414e2582017-09-14HMDB team, MONAView Spectrum
Experimental LC-MS/MSLC-MS/MS Spectrum - Linamarin Linear Ion Trap , positive-QTOFsplash10-0006-0390000000-790cec5ee5082b1549192017-09-14HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 10V, Positive-QTOFsplash10-00ks-9150000000-21a7a562083ca747be692016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 20V, Positive-QTOFsplash10-014r-9000000000-41f560bdd8b351dbae102016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 40V, Positive-QTOFsplash10-014i-9000000000-218d76388b6e2adf862b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 10V, Negative-QTOFsplash10-00l2-9260000000-8d2767506ce49eb7251a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 20V, Negative-QTOFsplash10-001i-9110000000-036fd16f5b6281c51d5b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 40V, Negative-QTOFsplash10-00lr-9000000000-2ef6f32d0883a3ce35e22016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 10V, Negative-QTOFsplash10-0002-0290000000-04e466e80fc34a31711f2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 20V, Negative-QTOFsplash10-014j-9430000000-938a48430e27b76573bb2021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 40V, Negative-QTOFsplash10-0api-9000000000-13d670ae474f26ad1b062021-09-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 10V, Positive-QTOFsplash10-0002-1970000000-9f82b8d658576c297dd82021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 20V, Positive-QTOFsplash10-014u-9400000000-bc1ee3aa7d00ae291fb12021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Linamarin 40V, Positive-QTOFsplash10-0uxu-9000000000-b040996bb0528ff708072021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB011809
KNApSAcK IDC00001446
Chemspider ID10657
KEGG Compound IDC01594
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkLinamarin
METLIN IDNot Available
PubChem Compound11128
PDB IDNot Available
ChEBI ID16441
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1837781
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

General function:
Involved in hydrolase activity, hydrolyzing O-glycosyl compounds
Specific function:
Glycosidase probably involved in the intestinal absorption and metabolism of dietary flavonoid glycosides. Able to hydrolyze a broad variety of glycosides including phytoestrogens, flavonols, flavones, flavanones and cyanogens. Possesses beta-glycosylceramidase activity and may be involved in a nonlysosomal catabolic pathway of glycosylceramide.
Gene Name:
GBA3
Uniprot ID:
Q9H227
Molecular weight:
Not Available
Reactions
Linamarin + Water → Acetone cyanohydrin + D-Glucosedetails