Bovine Metabolome Database: Showing metabocard for Phytosphingosine (BMDB0004610)

Identification Taxonomy Physical properties Pathways Spectra Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-09-30 23:09:46 UTC

Update Date

2020-05-11 20:57:18 UTC

BMDB ID

BMDB0004610

Secondary Accession Numbers

BMDB04610

Metabolite Identification

Common Name

Phytosphingosine

Description

Phytosphingosine, also known as SP(t18:0), belongs to the class of organic compounds known as 1,3-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 C3 atom. Thus, phytosphingosine is considered to be a sphingoid base lipid molecule. Phytosphingosine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. Phytosphingosine exists in all eukaryotes, ranging from yeast to humans.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
4-D-Hydroxysphinganine	ChEBI
4-R-Hydroxyoctadecasphinganine	ChEBI
(+)-D-Ribo-phytosphingosine	HMDB
4-D-Hydroxy-sphinganine	HMDB
4D-Hydroxysphinganine	HMDB
C18-Phytosphingosine	HMDB
D-Ribo-1,3,4-trihydroxy-2-aminooctadecane	HMDB
D-Ribo-2-amino-1,3,4-octadecanetriol	HMDB
[2S-(2R,3R,4S*)]-2-amino-1,3,4-octadecanetriol	HMDB
8-(Z-e)-C18-Phytosphingenine	HMDB
(2S,3S,4R)-2-Amino-1,3,4-octadecanetriol	HMDB
(2S,3S,4R)-2-Amino-1,3,4-trihydroxyoctadecane	HMDB
D-Ribo-phytosphingosine	HMDB
SP(t18:0)	HMDB
Phytosphingosine	HMDB

Chemical Formula

C₁₈H₃₉NO₃

Average Molecular Weight

317.5072

Monoisotopic Molecular Weight

317.292994119

IUPAC Name

(2S,3S,4R)-2-aminooctadecane-1,3,4-triol

Traditional Name

phytosphingosine

CAS Registry Number

554-62-1

SMILES

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

InChI Identifier

InChI=1S/C18H39NO3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17(21)18(22)16(19)15-20/h16-18,20-22H,2-15,19H2,1H3/t16-,17+,18-/m0/s1

InChI Key

AERBNCYCJBRYDG-KSZLIROESA-N

Chemical Taxonomy

Description

belongs to the class of organic compounds known as 1,3-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 C3 atom.

Kingdom

Organic compounds

Super Class

Organic nitrogen compounds

Class

Organonitrogen compounds

Sub Class

Amines

Direct Parent

1,3-aminoalcohols

Alternative Parents

Substituents

1,3-aminoalcohol
Secondary alcohol
1,2-aminoalcohol
Polyol
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

sphingoid (CHEBI:46961 )
amino alcohol (CHEBI:46961 )
triol (CHEBI:46961 )
4-Hydroxysphinganines (Phytosphingosines) (C12144 )
4-Hydroxysphinganines (Phytosphingosines) (LMSP01030001 )

Ontology

Status

Detected but not Quantified

Origin

Endogenous

Exogenous

Biofunction

Not Available

Application

Not Available

Cellular locations

Cell membrane
Membrane

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	102 - 103 °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	3.96	ALOGPS
logP	3.7	ChemAxon
logS	-3.8	ALOGPS
pKa (Strongest Acidic)	13.45	ChemAxon
pKa (Strongest Basic)	8.91	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	86.71 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	92.29 m³·mol⁻¹	ChemAxon
Polarizability	41.05 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-EI-TOF (Non-derivatized)	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0590000000-55f1259ff17447451d03	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0590000000-55f1259ff17447451d03	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fu-9240000000-f0c822bc0197665bc676	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0pxr-8498250000-59c3446ba7cde2700251	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 (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-03di-9025000000-41591a03203ebe6783ab	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-03yi-9055000000-c534f58f04d1f008079f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-014i-0009000000-2467642b22875f4e99a1	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-014i-0009000000-94b30bf1ae7ab25e566e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-03xr-9037000000-2e7ea43f8d534e10f1d4	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 15V, positive	splash10-03di-9020000000-ac9c04a9082abb540f22	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 19V, positive	splash10-03di-9010000000-e1fe657c8693bf3f19e7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 26V, positive	splash10-03di-9000000000-f71f3038d0b8478d679c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 31V, positive	splash10-03di-9000000000-795a4947f722e8f61620	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 38V, positive	splash10-03di-9000000000-e62d8c5bcb55aa166603	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 44V, positive	splash10-03di-9000000000-cb05f289ecdcd16de4e7	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 52V, positive	splash10-03di-9000000000-e898ac84341e318b5862	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 60V, positive	splash10-08fr-9000000000-b048fe168eacee259394	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 72V, positive	splash10-0900-9000000000-d72ddb3ba2da45266fab	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0udi-0039000000-33d42068332d814a2c83	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-06yt-6940000000-fdeb46044349d9fcc996	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0006-9000000000-981a59d4f1dd5e03c5ac	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0ik9-0190000000-d31bcfd06b73972a4300	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-03di-2290000000-b7855c3c2203ca25bab3	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-1029000000-ea43e68bb4fffc9657b1	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-9121000000-cce64d1dcf28012d72f8	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9520000000-d95a37794c98d95dd2b0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2097000000-1f5b8c8eefe1a491d0c9	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-9060000000-7550c32b4e1dfcbc4593	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9020000000-5cbe1fbb421cacd42e98	View in MoNA
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

Biological Properties

Cellular Locations

Cell membrane
Membrane

Biospecimen Locations

Blood
Epidermis
Liver
Placenta
Thyroid Gland

Pathways

Not Available

Name	SMPDB/Pathwhiz	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 25599412	details
Epidermis	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: 31873721	details
Liver	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	PMID: 31873721	details
Placenta	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

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Heat stress	PMID: 25913299	details

External Links

HMDB ID

HMDB0004610

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB023381

KNApSAcK ID

Not Available

Chemspider ID

108921

KEGG Compound ID

C12144

BioCyc ID

PHYTOSPINGOSINE

BiGG ID

Not Available

Wikipedia Link

Phytosphingosine

METLIN ID

7066

PubChem Compound

122121

PDB ID

Not Available

ChEBI ID

46961

References

Synthesis Reference

Mulzer, Johann; Brand, Clemens. Enantioselective syntheses of D- and L-ribo- and arabino-C18-phytosphingosine from (R)-2,3-O-isopropylideneglyceraldehyde. Tetrahedron (1986), 42(21), 5961-8.

Material Safety Data Sheet (MSDS)

Not Available

General References

Not Available

Showing metabocard for Phytosphingosine (BMDB0004610)

Structure for BMDB0004610 (Phytosphingosine)