Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2017-03-23 02:10:29 UTC
Update Date2021-09-14 14:59:49 UTC
HMDB IDHMDB0062485
Secondary Accession Numbers
  • HMDB62485
Metabolite Identification
Common NameLc3Cer
DescriptionN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-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 glycosyl-n-acylsphingosines. Glycosyl-N-acylsphingosines are compounds containing a sphingosine linked to a simple glucosyl moiety. N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-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?1563866318
Synonyms
ValueSource
N-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-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
Gal beta 1-4 glcna beta 1-3 gal beta 1-4 GLC-cerHMDB
NeolactotetraosylceramideHMDB
NLC(4)CerHMDB
NLC4CerHMDB
NLTCHMDB
ParaglobosideHMDB
Chemical FormulaC40H72N2O18
Average Molecular Weight869.012
Monoisotopic Molecular Weight868.478013486
IUPAC NameN-[(2S,3R)-1-{[(2R,3R,4R,5S,6R)-5-{[(2S,3R,4S,5S,6R)-4-{[(2S,3R,4R,5S,6R)-4,5-dihydroxy-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)-4,5-dihydroxy-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@]([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/C40H72N2O18/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-25(48)24(41-22(2)46)21-55-39-34(53)33(52)36(28(20-45)58-39)59-40-35(54)37(31(50)27(19-44)57-40)60-38-29(42-23(3)47)32(51)30(49)26(18-43)56-38/h16-17,24-40,43-45,48-54H,4-15,18-21H2,1-3H3,(H,41,46)(H,42,47)/t24-,25+,26+,27+,28+,29+,30+,31-,32+,33+,34+,35+,36+,37-,38-,39+,40-/m0/s1
InChI KeyIZUGJFIVXAZJFA-USLYCZPCSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycosyl-n-acylsphingosines. Glycosyl-N-acylsphingosines are compounds containing a sphingosine linked to a simple glucosyl moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassGlycosphingolipids
Direct ParentGlycosyl-N-acylsphingosines
Alternative Parents
Substituents
  • Glycosyl-n-acylsphingosine
  • Oligosaccharide
  • Fatty acyl glycoside
  • N-acyl-alpha-hexosamine
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Fatty acyl
  • Acetamide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Organoheterocyclic compound
  • Acetal
  • Carboxylic acid derivative
  • Oxacycle
  • Primary alcohol
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organonitrogen compound
  • Organooxygen compound
  • Carbonyl group
  • Organic nitrogen compound
  • Alcohol
  • 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 Solubility0.39 g/lALOGPS
LogP0.97ALOGPS
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP10(1.24) g/LALOGPS
logP10(0.42) g/LChemAxon
logS10(-3.8) g/LALOGPS
pKa (Strongest Acidic)5.36ChemAxon
pKa (Strongest Basic)2.51ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count20ChemAxon
Hydrogen Donor Count12ChemAxon
Polar Surface Area322.86 ŲChemAxon
Rotatable Bond Count26ChemAxon
Refractivity210.72 m³·mol⁻¹ChemAxon
Polarizability94.85 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+227.45430932474
DeepCCS[M-H]-225.80130932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Lc3Cer[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@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O5226.1Standard polar33892256
Lc3Cer[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@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O5999.6Standard non polar33892256
Lc3Cer[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@]([H])(O)[C@@]3([H])N=C(C)O)[C@@]2([H])O)[C@]([H])(O)[C@@]1([H])O)N=C(C)O5915.7Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 10V, Negative-QTOFsplash10-01b9-0000110090-f0e56ab5b9c1ba69deab2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 20V, Negative-QTOFsplash10-00b9-1201102290-9de795c7bd35b12e15b02021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 40V, Negative-QTOFsplash10-0a4i-9442310140-730ba78b3766c29ce2422021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 10V, Positive-QTOFsplash10-0gb9-1026000090-88ab21480528662fd7b42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 20V, Positive-QTOFsplash10-0fsi-2139100030-abad1b33816cff437f992021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Lc3Cer 40V, Positive-QTOFsplash10-000w-4912000000-ea58b1b25df3f04acfb32021-09-22Wishart 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 Compound57041562
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.