Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 21:31:12 UTC
Update Date2022-03-07 02:54:54 UTC
HMDB IDHMDB0036382
Secondary Accession Numbers
  • HMDB36382
Metabolite Identification
Common Name6-Deoxyfagomine
Description6-Deoxyfagomine 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. Based on a literature review very few articles have been published on 6-Deoxyfagomine.
Structure
Data?1563862867
Synonyms
ValueSource
(-)-6-Deoxy-fagomineHMDB
6-Deoxy-fagomineHMDB
Chemical FormulaC6H13NO2
Average Molecular Weight131.1729
Monoisotopic Molecular Weight131.094628665
IUPAC Name2-methylpiperidine-3,4-diol
Traditional Name2-methylpiperidine-3,4-diol
CAS Registry Number197449-09-5
SMILES
CC1NCCC(O)C1O
InChI Identifier
InChI=1S/C6H13NO2/c1-4-6(9)5(8)2-3-7-4/h4-9H,2-3H2,1H3
InChI KeyRMJCALHKIHCSMY-UHFFFAOYSA-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
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Amine
  • Alcohol
  • Organic oxygen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility1000000 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility542 g/LALOGPS
logP-0.93ALOGPS
logP-1.1ChemAxon
logS0.62ALOGPS
pKa (Strongest Acidic)13.51ChemAxon
pKa (Strongest Basic)9.21ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area52.49 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity33.93 m³·mol⁻¹ChemAxon
Polarizability14.09 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
DarkChem[M+H]+127.36131661259
DarkChem[M-H]-120.61131661259
DeepCCS[M+H]+132.11330932474
DeepCCS[M-H]-130.00730932474
DeepCCS[M-2H]-165.98230932474
DeepCCS[M+Na]+140.78730932474
AllCCS[M+H]+129.532859911
AllCCS[M+H-H2O]+124.832859911
AllCCS[M+NH4]+133.932859911
AllCCS[M+Na]+135.232859911
AllCCS[M-H]-125.632859911
AllCCS[M+Na-2H]-127.832859911
AllCCS[M+HCOO]-130.232859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
6-DeoxyfagomineCC1NCCC(O)C1O2266.0Standard polar33892256
6-DeoxyfagomineCC1NCCC(O)C1O1241.3Standard non polar33892256
6-DeoxyfagomineCC1NCCC(O)C1O1230.2Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
6-Deoxyfagomine,1TMS,isomer #1CC1NCCC(O[Si](C)(C)C)C1O1279.8Semi standard non polar33892256
6-Deoxyfagomine,1TMS,isomer #2CC1NCCC(O)C1O[Si](C)(C)C1315.0Semi standard non polar33892256
6-Deoxyfagomine,1TMS,isomer #3CC1C(O)C(O)CCN1[Si](C)(C)C1370.1Semi standard non polar33892256
6-Deoxyfagomine,2TMS,isomer #1CC1NCCC(O[Si](C)(C)C)C1O[Si](C)(C)C1386.8Semi standard non polar33892256
6-Deoxyfagomine,2TMS,isomer #2CC1C(O)C(O[Si](C)(C)C)CCN1[Si](C)(C)C1420.4Semi standard non polar33892256
6-Deoxyfagomine,2TMS,isomer #3CC1C(O[Si](C)(C)C)C(O)CCN1[Si](C)(C)C1432.3Semi standard non polar33892256
6-Deoxyfagomine,3TMS,isomer #1CC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CCN1[Si](C)(C)C1510.4Semi standard non polar33892256
6-Deoxyfagomine,3TMS,isomer #1CC1C(O[Si](C)(C)C)C(O[Si](C)(C)C)CCN1[Si](C)(C)C1531.9Standard non polar33892256
6-Deoxyfagomine,1TBDMS,isomer #1CC1NCCC(O[Si](C)(C)C(C)(C)C)C1O1527.7Semi standard non polar33892256
6-Deoxyfagomine,1TBDMS,isomer #2CC1NCCC(O)C1O[Si](C)(C)C(C)(C)C1548.9Semi standard non polar33892256
6-Deoxyfagomine,1TBDMS,isomer #3CC1C(O)C(O)CCN1[Si](C)(C)C(C)(C)C1630.7Semi standard non polar33892256
6-Deoxyfagomine,2TBDMS,isomer #1CC1NCCC(O[Si](C)(C)C(C)(C)C)C1O[Si](C)(C)C(C)(C)C1812.8Semi standard non polar33892256
6-Deoxyfagomine,2TBDMS,isomer #2CC1C(O)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C1876.5Semi standard non polar33892256
6-Deoxyfagomine,2TBDMS,isomer #3CC1C(O[Si](C)(C)C(C)(C)C)C(O)CCN1[Si](C)(C)C(C)(C)C1871.2Semi standard non polar33892256
6-Deoxyfagomine,3TBDMS,isomer #1CC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C2143.7Semi standard non polar33892256
6-Deoxyfagomine,3TBDMS,isomer #1CC1C(O[Si](C)(C)C(C)(C)C)C(O[Si](C)(C)C(C)(C)C)CCN1[Si](C)(C)C(C)(C)C2196.6Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 6-Deoxyfagomine GC-MS (Non-derivatized) - 70eV, Positivesplash10-074l-9300000000-210e4186cd3d9465ee032017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Deoxyfagomine GC-MS (2 TMS) - 70eV, Positivesplash10-074r-9850000000-64dd3aa9ea80f55467652017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 6-Deoxyfagomine 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 - 6-Deoxyfagomine 10V, Positive-QTOFsplash10-001i-1900000000-1eed61863fa3097ecbed2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Positive-QTOFsplash10-01qa-7900000000-d962f68c93310b6202842016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Positive-QTOFsplash10-052e-9000000000-1458ad075ed40e44ec532016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Negative-QTOFsplash10-001i-1900000000-d4c42898a0463209568f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Negative-QTOFsplash10-001i-7900000000-d169935340cb740ca3592016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Negative-QTOFsplash10-052f-9000000000-0c3793268633c265e2902016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Positive-QTOFsplash10-01q9-2900000000-d5b2f71dde168c0a84a12021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Positive-QTOFsplash10-0ac3-9300000000-3504d3b510ac2d8e24bc2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Positive-QTOFsplash10-0a4m-9000000000-8bbcfd71e2421f1be2fd2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 10V, Negative-QTOFsplash10-001i-0900000000-a42e42c2c7f8ddcd644f2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 20V, Negative-QTOFsplash10-059x-9400000000-3efa73ad5a65160c607b2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 6-Deoxyfagomine 40V, Negative-QTOFsplash10-052f-9000000000-d2335899b725a6fb17892021-09-23Wishart 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 IDFDB015260
KNApSAcK IDC00036613
Chemspider ID35014134
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound57449463
PDB IDNot Available
ChEBI ID172323
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1854901
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.. .