Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:11:15 UTC
Update Date2023-02-21 17:23:19 UTC
HMDB IDHMDB0033453
Secondary Accession Numbers
  • HMDB33453
Metabolite Identification
Common NameFagomine
DescriptionFagomine is an alkaloid found in the seeds of Castanospermum australe (commonly known as the Black Bean or the Moreton Bay Chestnut) (PMID: 25583438 ). Castanospermum australe is a large evergreen tree of the legume family native to the east coast of Australia in Queensland and New South Wales, and to the Pacific islands of Vanuatu, New Caledonia, and the island of New Britain (Papua New Guinea). The seeds are poisonous, but become edible when carefully prepared by roasting, cutting up into small pieces, leaching with running water for several days, and pounding into flour (Wikipedia).
Structure
Data?1677000199
Synonyms
ValueSource
D-FagomineChEMBL, HMDB
FagomineMeSH
1,2,5-Trideoxy-1,5-imino-D-arabino-hexitolMeSH, HMDB
(2R,3R,4R)-2-(Hydroxymethyl)-3,4-piperidinediolPhytoBank
Chemical FormulaC6H13NO3
Average Molecular Weight147.174
Monoisotopic Molecular Weight147.089543283
IUPAC Name(2R,3R,4R)-2-(hydroxymethyl)piperidine-3,4-diol
Traditional Namefagomine
CAS Registry Number53185-12-9
SMILES
OC[C@H]1NCC[C@@H](O)[C@@H]1O
InChI Identifier
InChI=1S/C6H13NO3/c8-3-4-6(10)5(9)1-2-7-4/h4-10H,1-3H2/t4-,5-,6-/m1/s1
InChI KeyYZNNBIPIQWYLDM-HSUXUTPPSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as piperidines. Piperidines are compounds containing a piperidine ring, which is a saturated aliphatic six-member ring with one nitrogen atom and five carbon atoms.
KingdomOrganic compounds
Super ClassOrganoheterocyclic compounds
ClassPiperidines
Sub ClassNot Available
Direct ParentPiperidines
Alternative Parents
Substituents
  • Piperidine
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Secondary aliphatic amine
  • Azacycle
  • Secondary amine
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Amine
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point186 - 188 °CNot Available
Boiling Point315.00 to 316.00 °C. @ 760.00 mm Hg (est)The Good Scents Company Information System
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP-0.880 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility573 g/LALOGPS
logP-1.6ALOGPS
logP-2.2ChemAxon
logS0.59ALOGPS
pKa (Strongest Acidic)13.43ChemAxon
pKa (Strongest Basic)8.63ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area72.72 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity35.48 m³·mol⁻¹ChemAxon
Polarizability15.06 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+134.66530932474
DeepCCS[M-H]-132.49930932474
DeepCCS[M-2H]-167.51430932474
DeepCCS[M+Na]+141.96530932474
AllCCS[M+H]+133.232859911
AllCCS[M+H-H2O]+128.732859911
AllCCS[M+NH4]+137.532859911
AllCCS[M+Na]+138.732859911
AllCCS[M-H]-127.332859911
AllCCS[M+Na-2H]-129.032859911
AllCCS[M+HCOO]-130.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
FagomineOC[C@H]1NCC[C@@H](O)[C@@H]1O2737.0Standard polar33892256
FagomineOC[C@H]1NCC[C@@H](O)[C@@H]1O1458.7Standard non polar33892256
FagomineOC[C@H]1NCC[C@@H](O)[C@@H]1O1525.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Fagomine,1TMS,isomer #1C[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O1515.5Semi standard non polar33892256
Fagomine,1TMS,isomer #2C[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O1519.7Semi standard non polar33892256
Fagomine,1TMS,isomer #3C[Si](C)(C)O[C@H]1[C@H](O)CCN[C@@H]1CO1500.1Semi standard non polar33892256
Fagomine,1TMS,isomer #4C[Si](C)(C)N1CC[C@@H](O)[C@H](O)[C@H]1CO1448.2Semi standard non polar33892256
Fagomine,2TMS,isomer #1C[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C)[C@@H]1O1581.8Semi standard non polar33892256
Fagomine,2TMS,isomer #2C[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O[Si](C)(C)C1555.1Semi standard non polar33892256
Fagomine,2TMS,isomer #3C[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O)CCN1[Si](C)(C)C1568.7Semi standard non polar33892256
Fagomine,2TMS,isomer #4C[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O[Si](C)(C)C1524.3Semi standard non polar33892256
Fagomine,2TMS,isomer #5C[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C)[C@H](CO)[C@H]1O1520.4Semi standard non polar33892256
Fagomine,2TMS,isomer #6C[Si](C)(C)O[C@H]1[C@H](O)CCN([Si](C)(C)C)[C@@H]1CO1533.5Semi standard non polar33892256
Fagomine,3TMS,isomer #1C[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C)[C@@H]1O[Si](C)(C)C1600.1Semi standard non polar33892256
Fagomine,3TMS,isomer #2C[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C1625.2Semi standard non polar33892256
Fagomine,3TMS,isomer #3C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O)CCN1[Si](C)(C)C1637.4Semi standard non polar33892256
Fagomine,3TMS,isomer #4C[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C)[C@H](CO)[C@H]1O[Si](C)(C)C1599.8Semi standard non polar33892256
Fagomine,4TMS,isomer #1C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C1698.6Semi standard non polar33892256
Fagomine,4TMS,isomer #1C[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C)[C@H](O[Si](C)(C)C)CCN1[Si](C)(C)C1792.0Standard non polar33892256
Fagomine,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O1761.4Semi standard non polar33892256
Fagomine,1TBDMS,isomer #2CC(C)(C)[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O1756.7Semi standard non polar33892256
Fagomine,1TBDMS,isomer #3CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)CCN[C@@H]1CO1748.7Semi standard non polar33892256
Fagomine,1TBDMS,isomer #4CC(C)(C)[Si](C)(C)N1CC[C@@H](O)[C@H](O)[C@H]1CO1735.6Semi standard non polar33892256
Fagomine,2TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O2025.5Semi standard non polar33892256
Fagomine,2TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O)[C@@H]1O[Si](C)(C)C(C)(C)C2004.7Semi standard non polar33892256
Fagomine,2TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O)CCN1[Si](C)(C)C(C)(C)C2032.1Semi standard non polar33892256
Fagomine,2TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1CCN[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C1985.5Semi standard non polar33892256
Fagomine,2TBDMS,isomer #5CC(C)(C)[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C(C)(C)C)[C@H](CO)[C@H]1O2008.3Semi standard non polar33892256
Fagomine,2TBDMS,isomer #6CC(C)(C)[Si](C)(C)O[C@H]1[C@H](O)CCN([Si](C)(C)C(C)(C)C)[C@@H]1CO2005.6Semi standard non polar33892256
Fagomine,3TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@H]1NCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@@H]1O[Si](C)(C)C(C)(C)C2257.2Semi standard non polar33892256
Fagomine,3TBDMS,isomer #2CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C2304.0Semi standard non polar33892256
Fagomine,3TBDMS,isomer #3CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O)CCN1[Si](C)(C)C(C)(C)C2289.8Semi standard non polar33892256
Fagomine,3TBDMS,isomer #4CC(C)(C)[Si](C)(C)O[C@@H]1CCN([Si](C)(C)C(C)(C)C)[C@H](CO)[C@H]1O[Si](C)(C)C(C)(C)C2271.3Semi standard non polar33892256
Fagomine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C2563.6Semi standard non polar33892256
Fagomine,4TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC[C@@H]1[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C2608.9Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Fagomine GC-MS (Non-derivatized) - 70eV, Positivesplash10-00ri-9400000000-3b8a5882645861b88c332017-07-27Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Fagomine GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 10V, Positive-QTOFsplash10-000t-0900000000-1cd0371a246b725601122017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 20V, Positive-QTOFsplash10-01q9-1900000000-bf1bf8f8fc28cdba567f2017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 40V, Positive-QTOFsplash10-03dl-9600000000-eb5b3f84b34a61c5ea292017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 10V, Negative-QTOFsplash10-0002-1900000000-d532dc64bdef94e8ec0a2017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 20V, Negative-QTOFsplash10-00mn-9700000000-01b152f05c6f3ed1cd4c2017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 40V, Negative-QTOFsplash10-0a4l-9000000000-c81ae5d7d7853799165f2017-06-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 10V, Negative-QTOFsplash10-0002-0900000000-f139716f16d745072c5a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 20V, Negative-QTOFsplash10-0a4j-9400000000-8a791e320b3bb834d1b62021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 40V, Negative-QTOFsplash10-0a4l-9000000000-54b85f2d100a98c86df42021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 10V, Positive-QTOFsplash10-03e9-0900000000-af1e57e01fc85eeb862f2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 20V, Positive-QTOFsplash10-001j-5900000000-f038cfecd4438da4f3252021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Fagomine 40V, Positive-QTOFsplash10-0a4i-9200000000-6fdcd83134b6d75373972021-09-24Wishart 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

IR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M-H]-)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+H]+)2023-02-04FELIX labView Spectrum
Predicted IR SpectrumIR Ion Spectrum (Predicted IRIS Spectrum, Adduct: [M+Na]+)2023-02-04FELIX 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 IDFDB011491
KNApSAcK IDC00002038
Chemspider ID65215
KEGG Compound IDC10144
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound72259
PDB IDNot Available
ChEBI ID4969
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1629151
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Kato A, Hirokami Y, Kinami K, Tsuji Y, Miyawaki S, Adachi I, Hollinshead J, Nash RJ, Kiappes JL, Zitzmann N, Cha JK, Molyneux RJ, Fleet GW, Asano N: Isolation and SAR studies of bicyclic iminosugars from Castanospermum australe as glycosidase inhibitors. Phytochemistry. 2015 Mar;111:124-31. doi: 10.1016/j.phytochem.2014.12.011. Epub 2015 Jan 9. [PubMed:25583438 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .