N-(26-Hydroxyhexacosanyl)phytosphingosine (YMDB00624)

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Identification

YMDB ID

YMDB00624

Name

N-(26-Hydroxyhexacosanyl)phytosphingosine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

N-(26-Hydroxyhexacosanyl)phytosphingosine belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine. N-(26-Hydroxyhexacosanyl)phytosphingosine is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Cer(t18:0/26:0(2-OH))
cer3_26
ceramide-3 (phytosphingosine:N-C26:2OH)
N-(2-hydroxyhexacosanoyl)-4S-hydroxysphinganine
N-(2-hydroxyhexacosanoyl)-phytoceramide

CAS number

Not Available

Weight

Average: 712.1812
Monoisotopic: 711.674074963

InChI Key

COPMYEMNKJZCGO-KZRDWULCSA-N

InChI

InChI=1S/C44H89NO5/c1-2-3-4-5-6-7-8-22-25-28-31-34-37-42(48)44(50)41(40-47)45-43(49)38-35-32-29-26-23-20-18-16-14-12-10-9-11-13-15-17-19-21-24-27-30-33-36-39-46/h41-42,44,46-48,50H,2-40H2,1H3,(H,45,49)/t41-,42+,44-/m0/s1

IUPAC Name

26-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide

Traditional IUPAC Name

26-hydroxy-N-[(2S,3S,4R)-1,3,4-trihydroxyoctadecan-2-yl]hexacosanamide

Chemical Formula

C₄₄H₈₉NO₅

SMILES

CCCCCCCCCCCCCC[C@@H](O)[C@@H](O)[C@H](CO)NC(=O)CCCCCCCCCCCCCCCCCCCCCCCCCO

Chemical Taxonomy

Description

belongs to the class of organic compounds known as phytoceramides. These are n-acylated 4-hydroxysphinganine.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Ceramides

Direct Parent

Phytoceramides

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 Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

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	6.4e-05 g/L	ALOGPS
logP	9.44	ALOGPS
logP	13.01	ChemAxon
logS	-7	ALOGPS
pKa (Strongest Acidic)	13.26	ChemAxon
pKa (Strongest Basic)	0.034	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	110.02 Å²	ChemAxon
Rotatable Bond Count	42	ChemAxon
Refractivity	214.11 m³·mol⁻¹	ChemAxon
Polarizability	97.09 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-Hexacosanoylphytosphingosine + NADPH + hydron + oxygen → NADP + N-(26-Hydroxyhexacosanyl)phytosphingosine + water

N-(26-Hydroxyhexacosanyl)phytosphingosine + 1D-myo-inositol 1-phosphate ↔ 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_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00kf-0016009200-1fff8b829529d137d1c3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-06rj-6416904000-11a7be8f2d4432a4ecd6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-4915100000-fa2630177f3fd476a9c4	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03e9-0032409600-42e0fc3e7ec9344c21ba	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0r0c-1042903000-45802daf22a6c5607e70	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9132100000-88adc38459b8d0152ae8	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	52374
HMDB ID	Not Available
Pubchem Compound ID	25271598
Kegg ID	Not Available
ChemSpider ID	23106997
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-(26-Hydroxyhexacosanyl)phytosphingosine (YMDB00624)

Structure for #<Compound:0xad9746c4>

Enzymes

Reactions

Reactions