Livestock Metabolome Database: Showing metabocard for Phytosphingosine (LMDB00456)

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

1.0

Creation Date

2016-07-13 19:50:15 UTC

Update Date

2016-09-23 18:45:30 UTC

Lmdb

LMDB00456

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Phytosphingosine

Description

Phytosphingosine is a phospholipid. Phospholipids are a class of lipids and a major component of all biological membranes; sphingolipid metabolites, such as sphingosine and ceramide, are highly bioactive compounds and are involved in diverse cell processes, including cell-cell interaction, cell proliferation, differentiation, and apoptosis. Phytosphingosine is also one of the most widely distributed natural sphingoid bases, which is abundant in fungi and plants, and also found in animals including animals. Phytosphingosine is structurally similar to sphingosine; phytosphingosine possesses a hydroxyl group at C-4 of the sphingoid long-chain base. The physiological roles of phytosphingosine are largely unknown. Phytosphingosine induces apoptosis in animal T-cell lymphoma and non-small cell lung cancer cells, and induces caspase-independent cytochrome c release from mitochondria. In the presence of caspase inhibitors, phytosphingosine-induced apoptosis is almost completely suppressed, suggesting that phytosphingosine-induced apoptosis is largely dependent on caspase activities. (PMID: 12576463 , 12531554 , 8046331 , 8048941 ,8706124 ).

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

Not Available

Biofunction

Not Available

Application

Not Available

Cellular locations

Not Available

Physical Properties

State

Not Available

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	3.96	ALOGPS
logP	3.7	ChemAxon
logS	-3.9	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	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0590000000-55f1259ff17447451d03	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	Spectrum
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0udi-0590000000-55f1259ff17447451d03	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-08fu-9240000000-f0c822bc0197665bc676	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-0pxr-8498250000-59c3446ba7cde2700251	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-03di-9025000000-41591a03203ebe6783ab	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-03yi-9055000000-c534f58f04d1f008079f	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-014i-0009000000-2467642b22875f4e99a1	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-014i-0009000000-94b30bf1ae7ab25e566e	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-03xr-9037000000-2e7ea43f8d534e10f1d4	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 15V, positive	splash10-03di-9020000000-ac9c04a9082abb540f22	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 19V, positive	splash10-03di-9010000000-e1fe657c8693bf3f19e7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 26V, positive	splash10-03di-9000000000-f71f3038d0b8478d679c	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 31V, positive	splash10-03di-9000000000-795a4947f722e8f61620	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 38V, positive	splash10-03di-9000000000-e62d8c5bcb55aa166603	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 44V, positive	splash10-03di-9000000000-cb05f289ecdcd16de4e7	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 52V, positive	splash10-03di-9000000000-e898ac84341e318b5862	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 60V, positive	splash10-08fr-9000000000-b048fe168eacee259394	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 72V, positive	splash10-0900-9000000000-d72ddb3ba2da45266fab	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0udi-0039000000-33d42068332d814a2c83	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-06yt-6940000000-fdeb46044349d9fcc996	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0006-9000000000-981a59d4f1dd5e03c5ac	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0ik9-0190000000-d31bcfd06b73972a4300	Spectrum
LC-MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-03di-2290000000-b7855c3c2203ca25bab3	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-1029000000-ea43e68bb4fffc9657b1	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-9121000000-cce64d1dcf28012d72f8	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9520000000-d95a37794c98d95dd2b0	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2097000000-1f5b8c8eefe1a491d0c9	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-9060000000-7550c32b4e1dfcbc4593	Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9020000000-5cbe1fbb421cacd42e98	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum
1D NMR	13C NMR Spectrum	Not Available	Spectrum
1D NMR	1H NMR Spectrum	Not Available	Spectrum

Biological Properties

Cellular Locations

Not Available

Biofluid Locations and Tissue Locations

Plasma
Serum

Concentrations

Biofluid	Status	Value	Condition	Species	Reference	Details
Plasma	Detected but not Quantified	Not Applicable	Not Available	Bovine	25913299	details
Serum	Detected but not Quantified	Not Applicable	Not Available	Bovine	25599412	details

External Links

DrugBank ID

Not Available

HMDB ID

HMDB0004610

FooDB ID

FDB023381

Phenol Explorer ID

Not Available

KNApSAcK ID

Not Available

BiGG ID

Not Available

BioCyc ID

PHYTOSPINGOSINE

METLIN ID

7066

PDB ID

Not Available

Wikipedia Link

Chemspider ID

ChEBI ID

PubChem Compound ID

Kegg Compound ID

YMDB ID

ECMDB ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Park MT, Kang JA, Choi JA, Kang CM, Kim TH, Bae S, Kang S, Kim S, Choi WI, Cho CK, Chung HY, Lee YS, Lee SJ: Phytosphingosine induces apoptotic cell death via caspase 8 activation and Bax translocation in human cancer cells. Clin Cancer Res. 2003 Feb;9(2):878-85. [12576463 ]
Maceyka M, Payne SG, Milstien S, Spiegel S: Sphingosine kinase, sphingosine-1-phosphate, and apoptosis. Biochim Biophys Acta. 2002 Dec 30;1585(2-3):193-201. [12531554 ]
Haimovitz-Friedman A, Kan CC, Ehleiter D, Persaud RS, McLoughlin M, Fuks Z, Kolesnick RN: Ionizing radiation acts on cellular membranes to generate ceramide and initiate apoptosis. J Exp Med. 1994 Aug 1;180(2):525-35. [8046331 ]
Quintans J, Kilkus J, McShan CL, Gottschalk AR, Dawson G: Ceramide mediates the apoptotic response of WEHI 231 cells to anti-immunoglobulin, corticosteroids and irradiation. Biochem Biophys Res Commun. 1994 Jul 29;202(2):710-4. [8048941 ]
Santana P, Pena LA, Haimovitz-Friedman A, Martin S, Green D, McLoughlin M, Cordon-Cardo C, Schuchman EH, Fuks Z, Kolesnick R: Acid sphingomyelinase-deficient human lymphoblasts and mice are defective in radiation-induced apoptosis. Cell. 1996 Jul 26;86(2):189-99. [8706124 ]

Showing metabocard for Phytosphingosine (LMDB00456)

Structure for LMDB00456 (Phytosphingosine)