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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2021-09-24 11:02:21 UTC
Update Date2021-09-24 11:02:21 UTC
HMDB IDHMDB0304602
Secondary Accession NumbersNone
Metabolite Identification
Common Name3-epi-Fagomine
Description3-epi-fagomine 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. 3-epi-fagomine is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a small amount of articles have been published on 3-epi-fagomine.
Structure
Thumb
Synonyms
ValueSource
3-EpifagomineChEBI
D-3-epi-FagominePhytoBank
(2R,3R,4S)-2-(Hydroxymethyl)-3,4-piperidinediolPhytoBank
Chemical FormulaC6H13NO3
Average Molecular Weight147.174
Monoisotopic Molecular Weight147.089543283
IUPAC Name(2R,3R,4S)-2-(hydroxymethyl)piperidine-3,4-diol
Traditional Name(2R,3R,4S)-2-(hydroxymethyl)piperidine-3,4-diol
CAS Registry NumberNot Available
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-NGJCXOISSA-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
  • 1,2-diol
  • Secondary alcohol
  • Secondary aliphatic amine
  • Azacycle
  • Secondary amine
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Amine
  • Primary alcohol
  • Organic oxygen compound
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
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
Polarizability14.86 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
AllCCS[M+H]+133.24332859911
AllCCS[M+H-H2O]+128.68632859911
AllCCS[M+Na]+138.7232859911
AllCCS[M+NH4]+137.49432859911
AllCCS[M-H]-127.33432859911
AllCCS[M+Na-2H]-129.02532859911
AllCCS[M+HCOO]-130.9432859911
DeepCCS[M+H]+135.36330932474
DeepCCS[M-H]-133.16830932474
DeepCCS[M-2H]-168.2630932474
DeepCCS[M+Na]+142.93630932474

Predicted Kovats Retention Indices

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-epi-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
3-epi-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
3-epi-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)C1743.1Standard polar33892256
3-epi-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
3-epi-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
3-epi-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)C2252.6Standard polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 10V, Positive-QTOFsplash10-000t-0900000000-b40800ba81e4d18475202019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 20V, Positive-QTOFsplash10-01q9-0900000000-c4b1c4dba77ca1e9db4b2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 40V, Positive-QTOFsplash10-03dl-9600000000-8c5cb8447ec19256a71c2019-02-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 10V, Negative-QTOFsplash10-0002-0900000000-d89b3217065b8df2f46e2019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 20V, Negative-QTOFsplash10-00kb-6900000000-36828f5fb706b6a4ddb12019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 40V, Negative-QTOFsplash10-0a4l-9000000000-5544c4cce17fb3d8d3022019-02-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 10V, Positive-QTOFsplash10-03e9-0900000000-af1e57e01fc85eeb862f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 20V, Positive-QTOFsplash10-001j-5900000000-f038cfecd4438da4f3252021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 40V, Positive-QTOFsplash10-0a4i-9200000000-6fdcd83134b6d75373972021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 10V, Negative-QTOFsplash10-0002-0900000000-f139716f16d745072c5a2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 20V, Negative-QTOFsplash10-0a4j-9400000000-8a791e320b3bb834d1b62021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-epi-Fagomine 40V, Negative-QTOFsplash10-0a4l-9000000000-54b85f2d100a98c86df42021-10-21Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDFDB093552
KNApSAcK IDC00049947
Chemspider ID8466336
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10290867
PDB IDNot Available
ChEBI ID132399
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available