Bovine Metabolome Database: Showing metabocard for Sphingosine (BMDB0000252)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (2) Show 2 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:27:26 UTC

Update Date

2020-05-11 20:52:36 UTC

BMDB ID

BMDB0000252

Secondary Accession Numbers

BMDB00252

Metabolite Identification

Common Name

Sphingosine

Description

Sphingosine, also known as (4e)-sphingenine, 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. Sphingosine exists as a solid, possibly soluble (in water), and a very strong basic compound (based on its pKa) molecule. Sphingosine exists in all eukaryotes, ranging from yeast to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(-)-D-Erythro-sphingosine	HMDB
(2S,3R)-Sphingosine	HMDB
(2S,3R,4E)-2-Amino-4-octadecene-1,3-diol	HMDB
(4E)-Sphingenine	HMDB
4-Sphingenine	HMDB
4-trans-Sphingenine	HMDB
[R-[R,s-(e)]]-2-amino-4-octadecene-1,3-diol	HMDB

Chemical Formula

C₁₈H₃₇NO₂

Average Molecular Weight

299.4919

Monoisotopic Molecular Weight

299.282429433

IUPAC Name

(4E)-2-aminooctadec-4-ene-1,3-diol

Traditional Name

sphingosine

CAS Registry Number

123-78-4

SMILES

CCCCCCCCCCCCC\C=C\C(O)C(N)CO

InChI Identifier

InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h14-15,17-18,20-21H,2-13,16,19H2,1H3/b15-14+

InChI Key

WWUZIQQURGPMPG-CCEZHUSRSA-N

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

Not Available

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Lysosome
Membrane
Mitochondria

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	81 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	5.15	ALOGPS
logP	4.57	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	14.12	ChemAxon
pKa (Strongest Basic)	9.23	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	15	ChemAxon
Refractivity	91.89 m³·mol⁻¹	ChemAxon
Polarizability	39.38 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03dr-9260000000-2ff04e0afd9e8b2f0851	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-003r-8915100000-51f94df9cbd9e00dbf76	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-001i-0090000000-67307f0b7f6f858af400	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0a59-9010000000-e66065dfabaedfa9a7f2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0api-9000000000-a5c7c01555839f61ab3d	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f89-0092000000-c0188d9e3166e42d0a72	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-02ai-2390000000-23fd78f38dca1695f653	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4m-6940000000-bd71a7546dbbc9a6e83b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-0090000000-310f8ec2f529dd63e5b7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-07d4-4090000000-3ec929924c6bbc7293e0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9030000000-c344fe4fe9af07abf710	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer

Biological Properties

Cellular Locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Lysosome
Membrane
Mitochondria

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney
Leukocyte
Liver
Mammary Gland
Milk
Placenta
Platelet
Skeletal Muscle
Spleen

Pathways

Name	SMPDB/Pathwhiz	KEGG
Sphingolipid Metabolism		Not Available

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Epidermis	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Fibroblasts	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Intestine	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Kidney	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Leukocyte	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Mammary Gland	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Milk	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 23438684	details
Placenta	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Platelet	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Skeletal Muscle	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000252

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021919

KNApSAcK ID

Not Available

Chemspider ID

4510275

KEGG Compound ID

C00319

BioCyc ID

Not Available

BiGG ID

Wikipedia Link

METLIN ID

PubChem Compound

PDB ID

Not Available

ChEBI ID

16393

References

Synthesis Reference

Obayashi, Michio; Schlosser, Manfred. An efficient synthesis of (2S,3R)- and (2S,3S)-sphingosine. Chemistry Letters (1985), (11), 1715-18.

Material Safety Data Sheet (MSDS)

Not Available

General References

Melzer N, Wittenburg D, Hartwig S, Jakubowski S, Kesting U, Willmitzer L, Lisec J, Reinsch N, Repsilber D: Investigating associations between milk metabolite profiles and milk traits of Holstein cows. J Dairy Sci. 2013 Mar;96(3):1521-34. doi: 10.3168/jds.2012-5743. [PubMed:23438684 ]

Enzymes

Enzyme Details

1. Acid ceramidase

General function:: Involved in ceramidase activity
Specific function:: Lysosomal ceramidase that hydrolyzes sphingolipid ceramides into sphingosine and free fatty acids at acidic pH (By similarity). Ceramides, sphingosine, and its phosphorylated form sphingosine-1-phosphate are bioactive lipids that mediate cellular signaling pathways regulating several biological processes including cell proliferation, apoptosis and differentiation (By similarity). Has a higher catalytic efficiency towards C12-ceramides versus other ceramides (By similarity). Also catalyzes the reverse reaction allowing the synthesis of ceramides from fatty acids and sphingosine (By similarity). For the reverse synthetic reaction, the natural sphingosine D-erythro isomer is more efficiently utilized as a substrate compared to D-erythro-dihydrosphingosine and D-erythro-phytosphingosine, while the fatty acids with chain lengths of 12 or 14 carbons are the most efficiently used (By similarity). Has also an N-acylethanolamine hydrolase activity (By similarity). By regulating the levels of ceramides, sphingosine and sphingosine-1-phosphate in the epidermis, mediates the calcium-induced differentiation of epidermal keratinocytes (By similarity). Also indirectly regulates tumor necrosis factor/TNF-induced apoptosis (By similarity). By regulating the intracellular balance between ceramides and sphingosine, in adrenocortical cells, probably also acts as a regulator of steroidogenesis (By similarity).
Gene Name:: ASAH1
Uniprot ID:: Q17QB3
Molecular weight:: 44965.0

Enzyme Details

2. Sphingosine 1-phosphate receptor 1

General function:: Involved in lysosphingolipid and lysophosphatidic acid
Specific function:: G-protein coupled receptor for the bioactive lysosphingolipid sphingosine 1-phosphate (S1P) that seems to be coupled to the G(i) subclass of heteromeric G proteins. Signaling leads to the activation of RAC1, SRC, PTK2/FAK1 and MAP kinases. Plays an important role in cell migration, probably via its role in the reorganization of the actin cytoskeleton and the formation of lamellipodia in response to stimuli that increase the activity of the sphingosine kinase SPHK1. Required for normal chemotaxis toward sphingosine 1-phosphate. Required for normal embryonic heart development and normal cardiac morphogenesis. Plays an important role in the regulation of sprouting angiogenesis and vascular maturation. Inhibits sprouting angiogenesis to prevent excessive sprouting during blood vessel development. Required for normal egress of mature T-cells from the thymus into the blood stream and into peripheral lymphoid organs. Plays a role in the migration of osteoclast precursor cells, the regulation of bone mineralization and bone homeostasis. Plays a role in responses to oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine by pulmonary endothelial cells and in the protection against ventilator-induced lung injury (By similarity).
Gene Name:: S1PR1
Uniprot ID:: Q5E9P3
Molecular weight:: 42949.0

Showing metabocard for Sphingosine (BMDB0000252)

Structure for BMDB0000252 (Sphingosine)

Enzymes