Sphinganine (YMDB00327)

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Identification

YMDB ID

YMDB00327

Name

Sphinganine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Sphinganine (dihydrosphingosine) is an intermediate in sphingolipid metabolism pathway. Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannosyl-diinositol-phosphorylceramide (M(IP)2C). Sphingolipid long chain bases (LCBs) - dihydrosphingosine (DHS) and phytosphingosine (PHS) - are implicated as secondary messengers in vital signaling pathways. [Biocyc SPHINGOLIPID-SYN-PWY]

Structure

MOL SDF PDB SMILES InChI

Synonyms

[R-(R*,S*)]-2-amino-1,3-Octadecanediol
2-amino-D-erythro-1,3-Octadecanediol
C18-dihydro-Sphingosine
C18-Dihydrosphingosine
D-erythro-1,3-Dihydroxy-2-aminooctadecane
D-erythro-2-Amino-1,3-octadecanediol
D-erythro-C18-Dihydrosphingosine
D-erythro-Sphinganine
Dihydro-C18-sphingosine
Dihydrosphingosine
erythro-Sphinganine
Octadecasphinganine
Sphinganine
(2S,3R)-2-Amino-1,3-octadecanediol
(2S,3R)-2-Aminooctadecane-1,3-diol
(R-(R*,s*))-2-aminooctadecane-1,3-diol
2-Amino-1,3-dihydroxyoctadecane
C18-Sphinganine
D18:0
Safingol
Erythro-D-sphinganine
2-Aminooctadecane-1,3-diol
Threo-dihydrosphingosine
(2S,3R)-Sphinganine
D-Erythro-dihydrosphingosine
SP(D18:0)

CAS number

764-22-7

Weight

Average: 301.5078
Monoisotopic: 301.298079497

InChI Key

OTKJDMGTUTTYMP-ZWKOTPCHSA-N

InChI

InChI=1S/C18H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17-18,20-21H,2-16,19H2,1H3/t17-,18+/m0/s1

IUPAC Name

(2S,3R)-2-aminooctadecane-1,3-diol

Traditional IUPAC Name

sphinganine

Chemical Formula

C₁₈H₃₉NO₂

SMILES

[H]OC([H])([H])[C@]([H])(N([H])[H])[C@]([H])(O[H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 1,2-aminoalcohols. These are organic compounds containing an alkyl chain with an amine group bound to the C1 atom and an alcohol group bound to the C2 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,2-aminoalcohols

Alternative Parents

Substituents

Secondary alcohol
1,2-aminoalcohol
Organic oxygen compound
Organopnictogen compound
Hydrocarbon derivative
Primary amine
Primary alcohol
Organooxygen compound
Primary aliphatic amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-aminooctadecane-1,3-diol (CHEBI:16566 )
Sphinganines (C00836 )
Sphinganines (LMSP01020001 )

Physical Properties

State

Solid

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	0.0045 g/L	ALOGPS
logP	5.2	ALOGPS
logP	4.77	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	14.42	ChemAxon
pKa (Strongest Basic)	9.29	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	66.48 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	90.93 m³·mol⁻¹	ChemAxon
Polarizability	40.68 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

endoplasmic reticulum

Organoleptic Properties

Not Available

SMPDB Pathways

Biosynthesis of unsaturated fatty acids	PW002403
Biosynthesis of unsaturated fatty acids (docosanoyl)	PW002408
Biosynthesis of unsaturated fatty acids (icosanoyl)	PW002434
Biosynthesis of unsaturated fatty acids (stearoyl)	PW002435
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)	PW002404

KEGG Pathways

Biosynthesis of unsaturated fatty acids	ec01040
Sphingolipid metabolism	ec00600

SMPDB Reactions

hydron + oxygen + ferrocytochrome b5 + Sphinganine → water + Phytosphingosine + ferricytochrome b5

hydron + NADPH + 3-Dehydrosphinganine → NADP + Sphinganine

Sphinganine + NADPH → 3-Dehydrosphinganine + NADP

Adenosine triphosphate + Sphinganine → ADP + Sphinganine 1-phosphate

Sphinganine 1-phosphate + ADP → Sphinganine + Adenosine triphosphate

KEGG Reactions

3-Dehydrosphinganine + NADPH + hydron ↔ Sphinganine + NADP

Sphinganine + Tetracosanoyl-CoA → N-tetracosanoylsphinganine + hydron + Coenzyme A

Sphinganine + hexacosanoyl-CoA → N-hexacosanylsphinganine + hydron + Coenzyme A

Sphinganine + NADPH + hydron + oxygen → NADP + Phytosphingosine + water

water + Sphinganine 1-phosphate → Sphinganine + phosphate

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-3980100000-87c0074f611dec416856	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-1690000000-8fed2f980c631302b97b	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-3980100000-87c0074f611dec416856	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-1690000000-8fed2f980c631302b97b	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9120000000-0cfd71520376dffc3c78	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0uk9-4490200000-f4c4281643554b83dd43	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0iml-3791000000-013fe5eb404ccb287385	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9000000000-04469479cb6d83603093	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0bt9-9000000000-4f682b26d6efc1673141	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0udi-0009000000-4d5daf40edf51d7c5ce4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0f89-2196000000-86bd4d9593c5a53dfc94	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-01qa-9130000000-819bc3df8d7408799b9f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-03xr-9000000000-0b47410c79f07946095a	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-03xr-9000000000-6dd6eb4c242974e7f7cc	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-qTof , Positive	splash10-0ab9-3892000000-6d8fa67090a1cebaa6f3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0159-0092000000-6e15bf1516b938239cb5	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0udi-0009000000-4d5daf40edf51d7c5ce4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0f89-2196000000-86bd4d9593c5a53dfc94	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-01qa-9130000000-819bc3df8d7408799b9f	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03xr-9000000000-3157cbca45e3dce158e4	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03xr-9000000000-6dd6eb4c242974e7f7cc	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-0udi-2390000000-a002411e49400899cf3c	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0gx0-5096000000-ad6ab79ab16fab02d693	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-08fr-9000000000-5afe9071156e7abc48f2	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 25V, Negative	splash10-0159-0092000000-9c001535e8080ffe05e2	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fsi-0092000000-4cad101913d628c296ba	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0159-2290000000-e693ddcd90fd9234c669	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06r7-9740000000-808c9a702fe97ec9078e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-1089000000-00c77e7cc5d9f3475be7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-115c-5091000000-dc391e96a566caaa0602	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9030000000-a74567f0d047f0915ffc	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
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
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
Dickson, R. C., Sumanasekera, C., Lester, R. L. (2006). "Functions and metabolism of sphingolipids in Saccharomyces cerevisiae." Prog Lipid Res 45:447-465.16730802
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:

Roush, William R.; Adam, Michael A. Directed openings of 2,3-epoxy alcohols via reactions with isocyanates: synthesis of (+)-erythro-dihydrosphingosine. Journal of Organic Chemistry (1985), 50(20), 3752-7.

External Links:

Resource	Link
CHEBI ID	16566
HMDB ID	HMDB00269
Pubchem Compound ID	3126
Kegg ID	C00836
ChemSpider ID	82609
FOODB ID	FDB030824
Wikipedia ID	Safingol
BioCyc ID	DIHYDRO-SPHINGOSINE

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. Sphingoid long chain base kinase 4

General function:: Involved in diacylglycerol kinase activity
Specific function:: Catalyzes the phosphorylation of the sphingoid long chain bases dihydrosphingosine (DHS or sphinganine) and phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate (DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively. Involved in the biosynthesis of sphingolipids and ceramides. Required with LCB3 for an effective incorporation of DHS into ceramides through a phosphorylation-dephosphorylation cycle. Involved in heat-induced transient cell cycle arrest. Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling. Involved in heat-stress resistance
Gene Name:: LCB4
Uniprot ID:: Q12246
Molecular weight:: 69638.60156

Reactions

ATP + sphinganine → ADP + sphinganine 1-phosphate.
ATP + phytosphingosine → ADP + phytosphingosine 1-phosphate.

Protein Details

5. Sphingoid long chain base kinase 5

General function:: Involved in diacylglycerol kinase activity
Specific function:: Catalyzes the phosphorylation of the sphingoid long chain bases dihydrosphingosine (DHS or sphinganine) and phytosphingosine (PHS) to form dihydrosphingosine 1-phosphate (DHS-1P) and phytosphingosine 1-phosphate (PHS-1P) respectively. Redundant to LCB4, is only responsible for few percent of the total activity. Involved in the biosynthesis of sphingolipids and ceramides. Involved in heat-induced transient cell cycle arrest. Accumulation of phosphorylated sphingoid long chain bases (LCBPs) stimulates calcium influx and activates calcineurin signaling. Involved in heat-stress resistance
Gene Name:: LCB5
Uniprot ID:: Q06147
Molecular weight:: 77564.60156

Reactions

ATP + sphinganine → ADP + sphinganine 1-phosphate.
ATP + phytosphingosine → ADP + phytosphingosine 1-phosphate.

Protein Details

6. 3-ketodihydrosphingosine reductase TSC10

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS)
Gene Name:: TSC10
Uniprot ID:: P38342
Molecular weight:: 35986.19922

Reactions

Sphinganine + NADP(+) → 3-dehydrosphinganine + NADPH.

Protein Details

7. Dihydrosphingosine 1-phosphate phosphatase LCB3

General function:: Involved in catalytic activity
Specific function:: Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling
Gene Name:: LCB3
Uniprot ID:: P47013
Molecular weight:: 47371.30078

Reactions

Protein Details

8. Dihydrosphingosine 1-phosphate phosphatase YSR3

General function:: Involved in catalytic activity
Specific function:: Dihydrosphingosine 1-phosphate phosphatase required for efficient ceramide synthesis from exogenous sphingoid bases. Involved in endocytosis and calcium-mediated signaling
Gene Name:: YSR3
Uniprot ID:: P23501
Molecular weight:: 46487.69922

Reactions

Protein Details

9. 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

Structure for #<Compound:0xaa9c8e84>

Enzymes

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