N-(24-hydroxytetracosanoyl)sphinganine (YMDB00620)

You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Identification

YMDB ID

YMDB00620

Name

N-(24-hydroxytetracosanoyl)sphinganine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

N-(24-Hydroxytetracosanoyl)sphinganine is a ceramide (a sphingolipid). Ceramides are found in high concentrations within the cell membrane of cells. Ceramides are composed of a sphingosine and a fatty acid. Ceramides are found in high concentrations within the cell membrane of cells. Caramides are known to promote transport of secretory vesicles from the ER to the Golgi apparatus. Sphingolipids like ceramide play import roles in lipid rafts which in yeast are responsible for delivering and sorting membrane bound proteins. Lipid rafts also play roles in membrane fusion during mating.[PMID: 16730802]

There are three major pathways of ceramide generation. The sphingomyelinase pathway uses an enzyme to breakdown IPC, MIPC and M(IP)2C in the cell membrane and release ceramide. The de novo pathway creates ceramide from less complex molecules. Ceramide generation can also occur through breakdown of complex sphingolipids that are ultimately broken down into sphingosine, which is then reused by reacylation to form ceramide. This latter pathway is termed the Salvage pathway.[Wikipedia, PMID: 16730802]

Structure

MOL SDF PDB SMILES InChI

Synonyms

cer2'_24
ceramide-2' (sphinganine:N-C24:2OH)
N-(2-hydroxytetracosanyl)-dihydrosphingosine

CAS number

Not Available

Weight

Average: 668.1286
Monoisotopic: 667.647860213

InChI Key

ZQGNZSWBCQGWAO-WVILEFPPSA-N

InChI

InChI=1S/C42H85NO4/c1-2-3-4-5-6-7-8-18-21-24-27-30-33-36-41(46)40(39-45)43-42(47)37-34-31-28-25-22-19-16-14-12-10-9-11-13-15-17-20-23-26-29-32-35-38-44/h40-41,44-46H,2-39H2,1H3,(H,43,47)/t40-,41+/m0/s1

IUPAC Name

N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]-24-hydroxytetracosanamide

Traditional IUPAC Name

N-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]-24-hydroxytetracosanamide

Chemical Formula

C₄₂H₈₅NO₄

SMILES

CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCO

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.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Ceramides

Direct Parent

Ceramides

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 Framework

Aliphatic acyclic compounds

External Descriptors

N-acylsphinganines (dihydroceramides) (LMSP02020017 )

Physical Properties

State

Not Available

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	4.2e-05 g/L	ALOGPS
logP	9.79	ALOGPS
logP	13.19	ChemAxon
logS	-7.2	ALOGPS
pKa (Strongest Acidic)	13.83	ChemAxon
pKa (Strongest Basic)	0.038	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	89.79 Å²	ChemAxon
Rotatable Bond Count	40	ChemAxon
Refractivity	203.55 m³·mol⁻¹	ChemAxon
Polarizability	91.8 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Golgi
endoplasmic reticulum

Organoleptic Properties

Not Available

SMPDB Pathways

Not Available

KEGG Pathways

Not Available

SMPDB Reactions

Not Available

KEGG Reactions

N-tetracosanoylsphinganine + NADPH + hydron + oxygen → NADP + water + N-(24-hydroxytetracosanoyl)sphinganine

1D-myo-inositol 1-phosphate + N-(24-hydroxytetracosanoyl)sphinganine ↔ inositol-P-ceramide C (C26)

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-0012009000-67c16451d9d8385a7bfb	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-1056109000-7919baffe64e0fcf1f7f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0udi-4759000000-fd4fc3c1d006001d4e6e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-0001009000-18d11a260338f0e9003d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-015a-0025209000-d7f595a80f7680e0ce9d	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9046000000-d26c6930c30b34d13381	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer

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:

Resource	Link
CHEBI ID	52371
HMDB ID	Not Available
Pubchem Compound ID	25271603
Kegg ID	Not Available
ChemSpider ID	23106994
FOODB ID	Not Available
Wikipedia ID	Not Available
BioCyc ID	Not 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

N-(24-hydroxytetracosanoyl)sphinganine (YMDB00620)

Structure for #<Compound:0xb0797664>

Enzymes

Reactions

Reactions