Bovine Metabolome Database: Showing metabocard for Sphinganine (BMDB0000269)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References enzymes (5) Show 5 proteins XML

Record Information

Version

1.0

Creation Date

2016-09-30 22:27:40 UTC

Update Date

2020-05-21 16:28:59 UTC

BMDB ID

BMDB0000269

Secondary Accession Numbers

BMDB00269

Metabolite Identification

Common Name

Sphinganine

Description

Sphinganine, also known as D18:0 or safingol, 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. Thus, sphinganine is considered to be a sphingoid base lipid molecule. Sphinganine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Sphinganine exists in all living species, ranging from bacteria to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
(2S,3R)-2-Amino-1,3-octadecanediol	ChEBI
(2S,3R)-2-Aminooctadecane-1,3-diol	ChEBI
(R-(R,s))-2-aminooctadecane-1,3-diol	ChEBI
2-Amino-1,3-dihydroxyoctadecane	ChEBI
C18-Dihydrosphingosine	ChEBI
C18-Sphinganine	ChEBI
D-Erythro-1,3-dihydroxy-2-aminooctadecane	ChEBI
D-Erythro-2-amino-1,3-octadecanediol	ChEBI
D-Erythro-C18-dihydrosphingosine	ChEBI
D18:0	ChEBI
Dihydrosphingosine	ChEBI
Octadecasphinganine	ChEBI
Safingol	ChEBI
Erythro-D-sphinganine	HMDB
2-Aminooctadecane-1,3-diol	HMDB
Threo-dihydrosphingosine	HMDB
2-Amino-D-erythro-1,3-octadecanediol	HMDB
C18-Dihydro-sphingosine	HMDB
D-Erythro-sphinganine	HMDB
Dihydro-C18-sphingosine	HMDB
Erythro-sphinganine	HMDB
[R-(R,s)]-2-amino-1,3-octadecanediol	HMDB
(2S,3R)-Sphinganine	HMDB
D-Erythro-dihydrosphingosine	HMDB
SP(D18:0)	HMDB
Sphinganine	HMDB

Chemical Formula

C₁₈H₃₉NO₂

Average Molecular Weight

301.5078

Monoisotopic Molecular Weight

301.298079497

IUPAC Name

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

Traditional Name

sphinganine

CAS Registry Number

764-22-7

SMILES

CCCCCCCCCCCCCCC[C@@H](O)[C@@H](N)CO

InChI Identifier

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

InChI Key

OTKJDMGTUTTYMP-ZWKOTPCHSA-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

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

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Cytoplasm
Endoplasmic reticulum
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	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	5.2	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	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
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-3980100000-87c0074f611dec416856	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (3 TMS)	splash10-0udi-1690000000-8fed2f980c631302b97b	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-3980100000-87c0074f611dec416856	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS (Non-derivatized)	splash10-0udi-1690000000-8fed2f980c631302b97b	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-03di-9120000000-0cfd71520376dffc3c78	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0uk9-4490200000-f4c4281643554b83dd43	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_1_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_1) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_2) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_3) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TBDMS_2_4) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0iml-3791000000-013fe5eb404ccb287385	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-03di-9000000000-04469479cb6d83603093	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)	splash10-0bt9-9000000000-4f682b26d6efc1673141	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive	splash10-0udi-0009000000-4d5daf40edf51d7c5ce4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive	splash10-0f89-2196000000-86bd4d9593c5a53dfc94	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive	splash10-01qa-9130000000-819bc3df8d7408799b9f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive	splash10-03xr-9000000000-0b47410c79f07946095a	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive	splash10-03xr-9000000000-6dd6eb4c242974e7f7cc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-qTof , Positive	splash10-0ab9-3892000000-6d8fa67090a1cebaa6f3	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT , negative	splash10-0159-0092000000-6e15bf1516b938239cb5	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0udi-0009000000-4d5daf40edf51d7c5ce4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-0f89-2196000000-86bd4d9593c5a53dfc94	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-01qa-9130000000-819bc3df8d7408799b9f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03xr-9000000000-3157cbca45e3dce158e4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , positive	splash10-03xr-9000000000-6dd6eb4c242974e7f7cc	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - , positive	splash10-0udi-2390000000-a002411e49400899cf3c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 10V, Positive	splash10-0gx0-5096000000-ad6ab79ab16fab02d693	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 40V, Positive	splash10-08fr-9000000000-5afe9071156e7abc48f2	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - 25V, Negative	splash10-0159-0092000000-9c001535e8080ffe05e2	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0fsi-0092000000-4cad101913d628c296ba	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0159-2290000000-e693ddcd90fd9234c669	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-06r7-9740000000-808c9a702fe97ec9078e	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0udi-1089000000-00c77e7cc5d9f3475be7	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-115c-5091000000-dc391e96a566caaa0602	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9030000000-a74567f0d047f0915ffc	View in MoNA
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD₃OD, experimental)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	Not Available	View in JSpectraViewer
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	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
Membrane

Biospecimen Locations

Epidermis
Fibroblasts
Intestine
Kidney
Liver
Placenta
Platelet
Spleen
Thyroid Gland

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
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31867104	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
Spleen	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details
Thyroid Gland	Expected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	Not Applicable	details

Abnormal Concentrations

Not Available

External Links

HMDB ID

HMDB0000269

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Safingol

METLIN ID

Not Available

PubChem Compound

91486

PDB ID

Not Available

ChEBI ID

16566

References

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.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Enzymes

Enzyme Details

1. 3-ketodihydrosphingosine reductase

General function:: Lipid transport and metabolism
Specific function:: Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS).
Gene Name:: KDSR
Uniprot ID:: Q2KIJ5
Molecular weight:: 36020.0

Reactions

Sphinganine + NADPH → 3-Dehydrosphinganine + NADP	details

Enzyme Details

2. Phospholipid phosphatase 2

General function:: Not Available
Specific function:: Magnesium-independent phospholipid phosphatase that catalyzes the dephosphorylation of a variety of glycerolipid and sphingolipid phosphate esters including phosphatidate/PA, lysophosphatidate/LPA, sphingosine 1-phosphate/S1P and ceramide 1-phosphate/C1P. Has no apparent extracellular phosphatase activity and therefore most probably acts intracellularly. Also acts on N-oleoyl ethanolamine phosphate/N-(9Z-octadecenoyl)-ethanolamine phosphate, a potential physiological compound. Through dephosphorylation of these bioactive lipid mediators produces new bioactive compounds and may regulate signal transduction in different cellular processes (By similarity). Indirectly regulates, for instance, cell cycle G1/S phase transition through its phospholipid phosphatase activity (By similarity).
Gene Name:: PLPP2
Uniprot ID:: Q2HJ61
Molecular weight:: 32328.0

Reactions

Sphinganine 1-phosphate + Water → Sphinganine + Hydrogen phosphate	details

Enzyme Details

3. Sphingosine kinase 2

General function:: Not Available
Specific function:: Not Available
Gene Name:: SPHK2
Uniprot ID:: E1BJM1
Molecular weight:: 69343.0

Reactions

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

Enzyme Details

4. Sphingosine-1-phosphate phosphatase 2

General function:: Not Available
Specific function:: Not Available
Gene Name:: SGPP2
Uniprot ID:: G3MXX9
Molecular weight:: 44782.0

Reactions

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

Enzyme Details

5. Alkaline ceramidase

General function:: Not Available
Specific function:: Hydrolyzes the sphingolipid ceramide into sphingosine and free fatty acid.
Gene Name:: ACER3
Uniprot ID:: A7MBH7
Molecular weight:: 31491.0

Reactions

Dihydroceramide → Sphinganine	details

Showing metabocard for Sphinganine (BMDB0000269)

Structure for BMDB0000269 (Sphinganine)

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions