Sphinganine 1-phosphate (YMDB00299)

Identification

YMDB ID

YMDB00299

Name

Sphinganine 1-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Sphinganine 1-phosphate (dihydrosphingosine 1-phosphate) 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

2-amino-3-hydroxyoctadecyl dihydrogen phosphate
Dihydrosphingosine 1-phosphate
dihydrosphingosine-1-phosphate
Sphinganine 1-phosphate
Sphinganine 1-phosphic acid
(2S,3R)-2-Amino-3-hydroxyoctadecyl dihydrogen phosphate
DHS-1P
DHS1p
(2S,3R)-2-Amino-3-hydroxyoctadecyl dihydrogen phosphoric acid
Dihydrosphingosine 1-phosphoric acid
Dihydrosphingosine-1-phosphoric acid
Sphinganine 1-phosphoric acid

CAS number

19794-97-9

Weight

Average: 381.4877
Monoisotopic: 381.264409907

InChI Key

YHEDRJPUIRMZMP-ZWKOTPCHSA-N

InChI

InChI=1S/C18H40NO5P/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(20)17(19)16-24-25(21,22)23/h17-18,20H,2-16,19H2,1H3,(H2,21,22,23)/t17-,18+/m0/s1

IUPAC Name

{[(2S,3R)-2-amino-3-hydroxyoctadecyl]oxy}phosphonic acid

Traditional IUPAC Name

dihydrosphingosine 1-phosphate

Chemical Formula

C₁₈H₄₀NO₅P

SMILES

[H]O[C@]([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])[C@@]([H])(N([H])[H])C([H])([H])OP(=O)(O[H])O[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Sphingolipids

Sub Class

Phosphosphingolipids

Direct Parent

Phosphosphingolipids

Alternative Parents

Substituents

Sphingoid-1-phosphate or derivatives
Phosphoethanolamine
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
1,2-aminoalcohol
Secondary alcohol
Organic nitrogen compound
Hydrocarbon derivative
Primary amine
Organic oxide
Organopnictogen compound
Organooxygen compound
Organonitrogen compound
Organic oxygen compound
Primary aliphatic amine
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

sphingoid 1-phosphate (CHEBI:16893 )
Sphingoid base 1-phosphates (C01120 )
Sphingoid base 1-phosphates (LMSP01050002 )

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	0.0057 g/L	ALOGPS
logP	3.8	ALOGPS
logP	3.64	ChemAxon
logS	-4.8	ALOGPS
pKa (Strongest Acidic)	1.52	ChemAxon
pKa (Strongest Basic)	9.75	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	113.01 Å²	ChemAxon
Rotatable Bond Count	18	ChemAxon
Refractivity	101.8 m³·mol⁻¹	ChemAxon
Polarizability	45.32 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

Sphingolipid metabolism

PW002479

KEGG Pathways

Sphingolipid metabolism

ec00600

SMPDB Reactions

Adenosine triphosphate + Sphinganine → ADP + Sphinganine 1-phosphate

Sphinganine 1-phosphate + ADP → Sphinganine + Adenosine triphosphate

Sphinganine 1-phosphate + water → Sphinganine + phosphate

Sphinganine 1-phosphate → O-Phosphoethanolamine + Palmitaldehyde

KEGG Reactions

Sphinganine 1-phosphate → Palmitaldehyde + O-Phosphoethanolamine

water + Sphinganine 1-phosphate → Sphinganine + phosphate

Sphinganine + Adenosine triphosphate → hydron + Sphinganine 1-phosphate + ADP

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 (Non-derivatized) - 70eV, Positive	splash10-0006-4910000000-711eb3339b5799f5551f	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-0006-9712000000-d3f905278b0c98d96e21	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0092000000-c380cef639a76f98b5d2	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0091000000-cd799d86547cdbc576fd	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - 20V, Positive	splash10-001i-0092000000-ca0e502c70b5513a4d0e	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-02ai-0096000000-dbafed0491e9c794b653	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0159-1191000000-8eba0bc6a08b306ade37	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dm-6980000000-5d1a644d3395595f3a2e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-003s-8019000000-89a5c40259a01d528cfe	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9010000000-c58d4e7b8dd266ebb800	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-67c93080b619a8be70dc	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-2009000000-f0dd423d086ac14ad6d6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-e1f5b79920ef4f1ff109	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-001i-2179000000-80cef27c29d75c429aa8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-014i-2190000000-46af6fd14fe789f145f9	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9110000000-3a5962a17ce1beb8cda7	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:

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
Mao, C., Xu, R., Bielawska, A., Szulc, Z. M., Obeid, L. M. (2000). "Cloning and characterization of a Saccharomyces cerevisiae alkaline ceramidase with specificity for dihydroceramide." J Biol Chem 275:31369-31378.10900202

Synthesis Reference:

Schick, Andreas; Kolter, Thomas; Giannis, Athanassios; Sandhoff, Konrad. Synthesis of phosphoramide analogs of sphinganine-1-phosphate. Tetrahedron (1996), 52(8), 2945-56.

External Links:

Resource	Link
CHEBI ID	16893
HMDB ID	HMDB01383
Pubchem Compound ID	520
Kegg ID	C01120
ChemSpider ID	23169036
FOODB ID	FDB022594
Wikipedia ID	Not Available
BioCyc ID	CPD-649

Enzymes

Protein Details

1. 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

2. 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

3. Sphingosine-1-phosphate lyase

General function:: Involved in carboxy-lyase activity
Specific function:: Cleaves phosphorylated sphingoid bases (PSBs), such as sphingosine-1-phosphate, into fatty aldehydes and phosphoethanolamine
Gene Name:: DPL1
Uniprot ID:: Q05567
Molecular weight:: 65565.10156

Reactions

Sphinganine 1-phosphate → phosphoethanolamine + palmitaldehyde.

Protein Details

4. 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

5. 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

Structure for #<Compound:0xafd0cf50>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions