N-(24-Hydroxytetracosanoyl)phytosphingosine (YMDB00623)

Identification
YMDB IDYMDB00623
NameN-(24-Hydroxytetracosanoyl)phytosphingosine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionN-(24-Hydroxytetracosanoyl)phytosphingosine belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine. N-(24-Hydroxytetracosanoyl)phytosphingosine is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • Cer(t18:0/24:0(2-OH))
  • cer3_24
  • ceramide-3 (phytosphingosine:N-C24:2OH)
  • N-(2-hydroxytetracosanoyl)-4S-hydroxysphinganine
  • N-(2-hydroxytetracosanoyl)-phytoceramide
CAS numberNot Available
WeightAverage: 684.128
Monoisotopic: 683.642774835
InChI KeyQSHYNGFWVLZFGM-LFVSMIGWSA-N
InChIInChI=1S/C42H85NO5/c1-2-3-4-5-6-7-8-20-23-26-29-32-35-40(46)42(48)39(38-45)43-41(47)36-33-30-27-24-21-18-16-14-12-10-9-11-13-15-17-19-22-25-28-31-34-37-44/h39-40,42,44-46,48H,2-38H2,1H3,(H,43,47)/t39-,40+,42-/m0/s1
IUPAC Name24-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tetracosanamide
Traditional IUPAC Name24-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tetracosanamide
Chemical FormulaC42H85NO5
SMILESCCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCO
Chemical Taxonomy
Description belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassCeramides
Direct ParentPhytoceramides
Alternative Parents
Substituents
  • N-acyl-4-hydroxysphinganine
  • Fatty acyl
  • N-acyl-amine
  • Fatty amide
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Polyol
  • Carboxylic acid derivative
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility8.9e-05 g/LALOGPS
logP9.26ALOGPS
logP12.12ChemAxon
logS-6.9ALOGPS
pKa (Strongest Acidic)13.26ChemAxon
pKa (Strongest Basic)0.034ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area110.02 ŲChemAxon
Rotatable Bond Count40ChemAxon
Refractivity204.91 m³·mol⁻¹ChemAxon
Polarizability92.81 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • Golgi
  • endoplasmic reticulum
Organoleptic PropertiesNot Available
SMPDB PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
N-Tetracosanoylphytosphingosine + NADPH + hydron + oxygen → N-(24-Hydroxytetracosanoyl)phytosphingosine + NADP + water
N-(24-Hydroxytetracosanoyl)phytosphingosine + 1D-myo-inositol 1-phosphate ↔ inositol-P-ceramide C (C26)
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_3_10) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0004009000-20e649a992784ddf1bfbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0cdi-6416904000-3b10762e815e866d1370JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-052b-5904100000-25a0a9f516962f0574e0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-053r-0021209000-5711d8e6a8ab419bfed4JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a4i-1065906000-3974c00758aeb8d65c60JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9134000000-73433ec7f25bd942a98bJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Funato, K., Vallee, B., Riezman, H. (2002). "Biosynthesis and trafficking of sphingolipids in the yeast Saccharomyces cerevisiae." Biochemistry 41:15105-15114.12484746
  • Reggiori, F., Conzelmann, A. (1998). "Biosynthesis of inositol phosphoceramides and remodeling of glycosylphosphatidylinositol anchors in Saccharomyces cerevisiae are mediated by different enzymes." J Biol Chem 273:30550-30559.9804825
  • Dickson, R. C. (2008). "Thematic review series: sphingolipids. New insights into sphingolipid metabolism and function in budding yeast." J Lipid Res 49:909-921.18296751
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52373
HMDB IDNot Available
Pubchem Compound ID25271597
Kegg IDNot Available
ChemSpider ID23106996
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Ceramide very long chain fatty acid hydroxylase SCS7
General function:
Involved in heme binding
Specific function:
Ceramide hydroxylase involved in the alpha-hydroxylation of sphingolipid-associated very long chain fatty acids. Hydroxylates the very long chain fatty acid of ceramides at C2 and C3
Gene Name:
SCS7
Uniprot ID:
Q03529
Molecular weight:
44881.10156
Reactions
Protein Details
2. Inositol phosphorylceramide synthase
General function:
Involved in catalytic activity
Specific function:
Catalyzes the addition of a phosphorylinositol group onto ceramide to form inositol phosphorylceramide, an essential step in sphingolipid biosynthesis
Gene Name:
AUR1
Uniprot ID:
P36107
Molecular weight:
45192.80078
Reactions