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N-tetracosanoylsphinganine (YMDB00619)

Identification
YMDB IDYMDB00619
NameN-tetracosanoylsphinganine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionCer(d18:0/24:0), also known as N-tetracosanoyl-sphinganine, is a ceramide (Cer). Ceramides are members of the class of compounds known as sphingolipids (SPs), or glycosylceramides. SPs are lipids containing a backbone of sphingoid bases (e.g. sphingosine or sphinganine) that are often covalently bound to a fatty acid derivative through N-acylation. SPs are found in cell membranes, particularly in peripheral nerve cells and the cells found in the central nervous system (including the brain and spinal cord). Sphingolipids are extremely versatile molecules that have functions controlling fundamental cellular processes such as cell division, differentiation, and cell death. Impairments associated with sphingolipid metabolism are associated with many common human diseases such as diabetes, various cancers, microbial infections, diseases of the cardiovascular and respiratory systems, Alzheimer’s disease and other neurological syndromes. The biosynthesis and catabolism of sphingolipids involves a large number of intermediate metabolites where many different enzymes are involved. Simple sphingolipids, which include the sphingoid bases and ceramides, make up the early products of the sphingolipid synthetic pathways, while complex sphingolipids may be formed by the addition of head groups to the ceramide template (Wikipedia). In humans, ceramides are phosphorylated to ceramide phosphates (CerPs) through the action of a specific ceramide kinase (CerK). Ceramide phosphates are important metabolites of ceramides as they act as a mediators of the inflammatory response. Ceramides are also one of the hydrolysis byproducts of sphingomyelins (SMs) through the action of the enzyme sphingomyelin phosphodiesterase, which has been identified in the subcellular fractions of human epidermis (PMID: 25935) and many other tissues. Ceramides can also be synthesized from serine and palmitate in a de novo pathway and are regarded as important cellular signals for inducing apoptosis (PMID: 14998372). Ceramides are key in the biosynthesis of glycosphingolipids and gangliosides. In terms of its appearance and structure, Cer(d18:0/24:0) is a colorless solid that consists of a saturated 18-carbon sphingoid base with an attached saturated tetracosanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • C24DH Cer
  • Cer(d18:0/24:0)
  • ceramide-1 (sphinganine:N-C24:0)
  • N-(tetracosanoyl)-sphinganine
  • Ceramide
  • Ceramide(D18:0/24:0)
  • N-(Tetracosanoyl)-dihydrosphingosine
  • N-(Tetracosanoyl)-D-erythro-sphinganine
CAS numberNot Available
WeightAverage: 652.1292
Monoisotopic: 651.652945591
InChI KeyBPLYVSYSBPLDOA-WVILEFPPSA-N
InChIInChI=1S/C42H85NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-26-28-30-32-34-36-38-42(46)43-40(39-44)41(45)37-35-33-31-29-27-25-16-14-12-10-8-6-4-2/h40-41,44-45H,3-39H2,1-2H3,(H,43,46)/t40-,41+/m0/s1
IUPAC NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]tetracosanamide
Traditional IUPAC NameC24DH cer
Chemical FormulaC42H85NO3
SMILESCCCCCCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](CO)[C@H](O)CCCCCCCCCCCCCCC
Chemical Taxonomy
Description belongs to the class of organic compounds known as ceramides. These are lipid molecules containing a sphingosine in which the amine group is linked to a fatty acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassCeramides
Direct ParentCeramides
Alternative Parents
Substituents
  • Ceramide
  • Fatty amide
  • N-acyl-amine
  • Fatty acyl
  • Carboxamide group
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Carboxylic acid derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Alcohol
  • Organic nitrogen compound
  • Carbonyl group
  • 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 Solubility2.2e-05 g/LALOGPS
logP10.25ALOGPS
logP14.63ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)13.83ChemAxon
pKa (Strongest Basic)0.034ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count39ChemAxon
Refractivity201.62 m³·mol⁻¹ChemAxon
Polarizability90.91 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 PathwaysNot Available
KEGG PathwaysNot Available
SMPDB ReactionsNot Available
KEGG Reactions
N-tetracosanoylsphinganine + NADPH + hydron + oxygen → NADP + N-Tetracosanoylphytosphingosine + water
N-tetracosanoylsphinganine + NADPH + hydron + oxygen → NADP + water + N-(24-hydroxytetracosanoyl)sphinganine
Sphinganine + Tetracosanoyl-CoA → N-tetracosanoylsphinganine + hydron + Coenzyme A
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ("Cer(d18:0/24:0),1TMS,#1" TMS) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000009000-9574b870066ad6a24b9dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0uxr-0050009000-26249c0203b2883e2fd0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00lr-0090005000-46bc4fc32af3616dbdb0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0000009000-01187e09d40ba7f7b0e2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0uxr-0050009000-37a02838e942a6634e1bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00lr-0090005000-dd9a9cd1a78fc9f64414JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0a4i-0000009000-42f1dcf9e64b812e1cd1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0a4i-0000009000-42f1dcf9e64b812e1cd1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-0000009000-4f89f56f2c517a99b6bcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-0000009000-5757f898b5d6a927658bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0udi-0010009000-42b0f13f3c2ca2c6b0f8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0gb9-0022009000-e2c423df118a0ac7836aJSpectraViewer
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
  • 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
  • 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 ID52961
HMDB IDHMDB0011768
Pubchem Compound ID5283577
Kegg IDNot Available
ChemSpider ID4446690
FOODB IDFDB028438
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. 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
4. 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
5. 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