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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-23 02:54:24 UTC
Update Date2021-09-14 14:59:49 UTC
HMDB IDHMDB0062506
Secondary Accession Numbers
  • HMDB62506
Metabolite Identification
Common NamenLc5Cer
DescriptionN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.g. S-,C-, or N-type) has been reported. N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid is a moderately basic compound (based on its pKa).
Structure
Data?1563866321
Synonyms
ValueSource
N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidateGenerator
Chemical FormulaC52H92N2O28
Average Molecular Weight1193.294
Monoisotopic Molecular Weight1192.58366033
IUPAC NameN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid
Traditional NameN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-3,5-dihydroxy-6-(hydroxymethyl)-4-{[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}oxan-2-yl]oxy}-4-hydroxy-3-[(1-hydroxyethylidene)amino]-6-(hydroxymethyl)oxan-2-yl]oxy}-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3,4-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-3-hydroxyoctadec-4-en-2-yl]ethanimidic acid
CAS Registry NumberNot Available
SMILES
[H]C(CCCCCCCCCCCCC)=C([H])[C@@]([H])(O)[C@]([H])(CO[C@]1([H])O[C@]([H])(CO)[C@@]([H])(O[C@]2([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@]3([H])O[C@]([H])(CO)[C@@]([H])(O[C@]4([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O[C@@]5([H])O[C@]([H])(CO)[C@]([H])(O)[C@]([H])(O)[C@@]5([H])O)[C@@]4([H])O)[C@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O
InChI Identifier
InChI=1S/C52H92N2O28/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-27(62)26(53-24(2)60)23-73-49-41(70)39(68)45(32(22-59)78-49)80-52-42(71)46(35(64)29(19-56)76-52)81-48-33(54-25(3)61)37(66)44(31(21-58)77-48)79-51-43(72)47(36(65)30(20-57)75-51)82-50-40(69)38(67)34(63)28(18-55)74-50/h16-17,26-52,55-59,62-72H,4-15,18-23H2,1-3H3,(H,53,60)(H,54,61)/t26-,27+,28+,29+,30+,31+,32+,33+,34-,35-,36-,37+,38-,39+,40+,41+,42+,43+,44+,45+,46-,47-,48-,49+,50+,51-,52-/m0/s1
InChI KeyHMOQZEGDEFENEX-WATINQGFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosphingolipids. These are sphingolipids containing a saccharide moiety glycosidically attached to the sphingoid base. Although saccharide moieties are mostly O-glycosidically linked to the ceramide moiety, other sphingolipids with glycosidic bonds of other types (e.G. S-,C-, or N-type) has been reported.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGlycosphingolipids
Alternative Parents
Substituents
  • Glycosphingolipid
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Fatty acyl
  • Oxane
  • Secondary alcohol
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid
  • Carboximidic acid derivative
  • Oxacycle
  • Acetal
  • Polyol
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Alcohol
  • Organic oxygen compound
  • Primary alcohol
  • Organopnictogen compound
  • Aliphatic heteromonocyclic compound
Molecular FrameworkAliphatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source

Route of exposure

Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility3.81 g/lALOGPS
LogP-0.12ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP10(0.24) g/LALOGPS
logP10(-3.1) g/LChemAxon
logS10(-2.7) g/LALOGPS
pKa (Strongest Acidic)5.3ChemAxon
pKa (Strongest Basic)2.51ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count30ChemAxon
Hydrogen Donor Count18ChemAxon
Polar Surface Area481.16 ŲChemAxon
Rotatable Bond Count32ChemAxon
Refractivity275.55 m³·mol⁻¹ChemAxon
Polarizability125.49 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 10V, Positive-QTOFsplash10-0w4i-3902320040-be010c1d1f8f0285bd052017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 20V, Positive-QTOFsplash10-0w2i-6709654080-df837613cfc952340e462017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 40V, Positive-QTOFsplash10-0w29-3916470060-8750def99c50d4b0b43f2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 10V, Negative-QTOFsplash10-03mm-2914722520-0b24aafcd1a4600a7f002017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 20V, Negative-QTOFsplash10-0fk9-3901221030-ebfff113f8b8ec0c478b2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 40V, Negative-QTOFsplash10-0udi-5633290510-2d914a5424c5fc7796cd2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 10V, Negative-QTOFsplash10-0007-0900010020-ffbf393e269ef60993892021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 20V, Negative-QTOFsplash10-0005-2900000000-473b24177e0ebac0d0152021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 40V, Negative-QTOFsplash10-0a59-9713130030-daea3bbb24efd120cda22021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 10V, Positive-QTOFsplash10-002f-2906012010-3d863d098f06151a07c62021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 20V, Positive-QTOFsplash10-06tg-2915141210-9a9383bd5bea4f6ba56c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - nLc5Cer 40V, Positive-QTOFsplash10-000w-3911000000-28af2892837a8e3888042021-09-23Wishart 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 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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
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 References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  7. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  8. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.