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N-hexacosanylsphinganine (YMDB00621)

Identification
YMDB IDYMDB00621
NameN-hexacosanylsphinganine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionCer(d18:0/26:0), also known as N-hexacosanoyl-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(d18:0/26:0) is a colorless solid that consists of a saturated 18-carbon sphingoid base with an attached saturated hexacosanoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • C26DH Cer
  • Cer(d18:0/26:0)
  • ceramide-1 (sphinganine:N-C26:0)
  • N-(hexacosanoyl)-sphinganine
  • N-[(2S,3R)-1,3-Bis(oxidanyl)octadecan-2-yl]hexacosanamide
  • Ceramide
  • Ceramide(D18:0/26:0)
  • N-(Hexacosanoyl)-dihydrosphingosine
  • N-(Hexacosanoyl)-D-erythro-sphinganine
CAS numberNot Available
WeightAverage: 680.1824
Monoisotopic: 679.684245719
InChI KeyNWERZHCPHDHUMO-WZYYJWNZSA-N
InChIInChI=1S/C44H89NO3/c1-3-5-7-9-11-13-15-17-18-19-20-21-22-23-24-25-26-28-30-32-34-36-38-40-44(48)45-42(41-46)43(47)39-37-35-33-31-29-27-16-14-12-10-8-6-4-2/h42-43,46-47H,3-41H2,1-2H3,(H,45,48)/t42-,43+/m0/s1
IUPAC NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]hexacosanamide
Traditional IUPAC NameC26DH cer
Chemical FormulaC44H89NO3
SMILESCCCCCCCCCCCCCCCCCCCCCCCCCC(=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 Solubility2.0e-05 g/LALOGPS
logP10.35ALOGPS
logP15.52ChemAxon
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 Count41ChemAxon
Refractivity210.82 m³·mol⁻¹ChemAxon
Polarizability95.16 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-hexacosanylsphinganine + NADPH + hydron + oxygen → NADP + N-Hexacosanoylphytosphingosine + water
N-hexacosanylsphinganine + NADPH + hydron + oxygen → NADP + water + N-(26-hydroxyhexacosanoyl)sphinganine
Sphinganine + hexacosanoyl-CoA → N-hexacosanylsphinganine + 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 LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0000009000-04d4b2058d5dd4e56263JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00lr-0050009000-43e32de57e52a16be004JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02u0-0090005000-ae017d870733c1732928JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-001i-0000009000-4b32edfaf68dd5b333b2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00lr-0050009000-cb93188c0e88c9e47519JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-02u0-0090005000-85657e5f126099809a47JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-004i-0000009000-0345db465d753bb73c0bJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-0010009000-05ffe05b233028ff0300JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004k-0022009000-6ca0bbe7d91ff99f5becJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0000009000-5076f28db2bfa2294cd3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0000009000-5076f28db2bfa2294cd3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-0000009000-d21a54b4ed276b4e7fe9JSpectraViewer
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 ID52962
HMDB IDHMDB0011771
Pubchem Compound ID644245
Kegg IDNot Available
ChemSpider ID559264
FOODB IDFDB028441
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