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N-Tetracosanoylphytosphingosine (YMDB00963)

Identification
YMDB IDYMDB00963
NameN-Tetracosanoylphytosphingosine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionN-tetracosanoylphytosphingosine, also known as cer2_24 or ceramide-2 (phytosphingosine:n-C24:0), belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine. Thus, N-tetracosanoylphytosphingosine is considered to be a ceramide lipid molecule. N-tetracosanoylphytosphingosine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • cer2_24
  • ceramide-2 (phytosphingosine:N-C24:0)
  • (2S,3S,4R)-N-Tetracosanoyl-2-amino-1,3,4-octadecanetriol
  • N-(Tetracosanoyl)-4R-hydroxysphinganine
  • N-Tetracosanoyl-4-hydroxysphinganine
CAS numberNot Available
WeightAverage: 668.1286
Monoisotopic: 667.647860213
InChI KeyZESJDNWGTANZCC-LFVSMIGWSA-N
InChIInChI=1S/C42H85NO4/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-27-29-31-33-35-37-41(46)43-39(38-44)42(47)40(45)36-34-32-30-28-26-16-14-12-10-8-6-4-2/h39-40,42,44-45,47H,3-38H2,1-2H3,(H,43,46)/t39-,40+,42-/m0/s1
IUPAC NameN-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tetracosanamide
Traditional IUPAC NameN-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]tetracosanamide
Chemical FormulaC42H85NO4
SMILESCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)[C@H](O)CCCCCCCCCCCCCC
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 amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxylic acid derivative
  • Polyol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • Primary alcohol
  • Hydrocarbon derivative
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility4.4e-05 g/LALOGPS
logP9.88ALOGPS
logP13.55ChemAxon
logS-7.2ALOGPS
pKa (Strongest Acidic)13.26ChemAxon
pKa (Strongest Basic)0.029ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area89.79 ŲChemAxon
Rotatable Bond Count39ChemAxon
Refractivity202.98 m³·mol⁻¹ChemAxon
Polarizability91.74 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • endoplasmic reticulum
Organoleptic PropertiesNot Available
SMPDB Pathways
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)PW002404 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG PathwaysNot Available
SMPDB Reactions
Phytosphingosine + Tetracosanoyl-CoA → hydron + Coenzyme A + N-Tetracosanoylphytosphingosine
KEGG Reactions
N-tetracosanoylsphinganine + NADPH + hydron + oxygen → NADP + N-Tetracosanoylphytosphingosine + water
Phytosphingosine + Tetracosanoyl-CoA → N-Tetracosanoylphytosphingosine + hydron + Coenzyme A
N-Tetracosanoylphytosphingosine + NADPH + hydron + oxygen → N-(24-Hydroxytetracosanoyl)phytosphingosine + NADP + water
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0gb9-0005009000-44b5a42b9c2cfe1e7f5eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-7219402000-5e0c06d572636536e138JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03ka-6839511000-5ef26d0c02c4fa9e7992JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-0022209000-d14b6f7267d2da990aeeJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0aor-2069604000-c5e5512899e18d03575dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0aou-9133000000-8c71e1ac8b621b981528JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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
  • Mao, C., Xu, R., Bielawska, A., Szulc, Z. M., Obeid, L. M. (2000). "Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide." J Biol Chem 275:31369-31378.10900202
  • Jiang, J. C., Kirchman, P. A., Zagulski, M., Hunt, J., Jazwinski, S. M. (1998). "Homologs of the yeast longevity gene LAG1 in Caenorhabditis elegans and human." Genome Res 8:1259-1272.9872981
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52979
HMDB IDNot Available
Pubchem Compound ID10462091
Kegg IDNot Available
ChemSpider IDNot Available
FOODB IDNot Available
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Alkaline ceramidase YDC1
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Specific function:
Catalyzes the conversion of dihydroceramide and also phytoceramide to dihydrosphingosine or phytosphingosine. Prefers dihydroceramide. Very low reverse hydrolysis activity, catalyzing synthesis of dihydroceramide from fatty acid and dihydrosphingosine. Is not responsible for the breakdown of unsaturated ceramide. May play a role in heat stress response
Gene Name:
YDC1
Uniprot ID:
Q02896
Molecular weight:
37230.5
Reactions
Protein Details
2. Sphingosine N-acyltransferase LAG1
General function:
Involved in protein binding
Specific function:
Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAC1. Facilitates ER-to-Golgi transport of GPI-anchored proteins. Involved in the aging process. Deletion of LAG1 results in a pronounced increase (approximately 50%) in mean and in maximum life span
Gene Name:
LAG1
Uniprot ID:
P38703
Molecular weight:
48454.10156
Reactions
Acyl-CoA + sphingosine → CoA + N-acylsphingosine.
Protein Details
3. Alkaline ceramidase YPC1
General function:
Involved in hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
Specific function:
Hydrolyzes phytoceramide and also dihydroceramide into phytosphingosine or dihydrosphingosine. Prefers phytoceramide. Has also reverse hydrolysis activity, catalyzing synthesis of phytoceramide and dihydroceramide from palmitic acid and phytosphingosine or dihydrosphingosine. Is not responsible for the breakdown of unsaturated ceramide
Gene Name:
YPC1
Uniprot ID:
P38298
Molecular weight:
36419.39844
Reactions
Protein Details
4. Sphingosine N-acyltransferase LAC1
General function:
Involved in identical protein binding
Specific function:
Component of the ceramide synthase complex required for C26-CoA-dependent ceramide synthesis. Redundant with LAG1. Facilitates ER-to-Golgi transport of GPI-anchored proteins
Gene Name:
LAC1
Uniprot ID:
P28496
Molecular weight:
48991.60156
Reactions
Acyl-CoA + sphingosine → CoA + N-acylsphingosine.
Protein Details
5. Sphingolipid C4-hydroxylase SUR2
General function:
Involved in iron ion binding
Specific function:
Required for hydroxylation of C-4 in the sphingoid moiety of ceramide. Involved in the response to syringomycin
Gene Name:
SUR2
Uniprot ID:
P38992
Molecular weight:
40734.0
Reactions
Protein Details
6. 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