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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2006-08-13 22:13:39 UTC
Update Date2018-03-28 17:00:48 UTC
HMDB IDHMDB0004610
Secondary Accession Numbers
  • HMDB04610
Metabolite Identification
Common NamePhytosphingosine
DescriptionPhytosphingosine 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 humans. 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 human 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
Thumb
Synonyms
ValueSource
4-D-HydroxysphinganineChEBI
4-R-HydroxyoctadecasphinganineChEBI
(+)-D-ribo-PhytosphingosineHMDB
4-D-Hydroxy-sphinganineHMDB
4D-HydroxysphinganineHMDB
C18-PhytosphingosineHMDB
D-ribo-1,3,4-Trihydroxy-2-aminooctadecaneHMDB
D-ribo-2-amino-1,3,4-OctadecanetriolHMDB
[2S-(2R*,3R*,4S*)]-2-amino-1,3,4-octadecanetriolHMDB
8-(Z-e)-C18-PhytosphingenineMeSH
Chemical FormulaC18H39NO3
Average Molecular Weight317.5072
Monoisotopic Molecular Weight317.292994119
IUPAC Name(2S,3S,4R)-2-aminooctadecane-1,3,4-triol
Traditional Namephytosphingosine
CAS Registry Number554-62-1
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 KeyAERBNCYCJBRYDG-KSZLIROESA-N
Chemical Taxonomy
DescriptionThis compound 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.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassAmines
Direct Parent1,3-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 FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point102 - 103 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.045 g/LALOGPS
logP3.96ALOGPS
logP3.7ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)13.45ChemAxon
pKa (Strongest Basic)8.91ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area86.71 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity92.29 m³·mol⁻¹ChemAxon
Polarizability40.99 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-001i-1910000000-6a156f8b67eb8d2e2af8View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Non-derivatized)splash10-0udi-0590000000-55f1259ff17447451d03View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-08fu-9240000000-f0c822bc0197665bc676View in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0pxr-8498250000-59c3446ba7cde2700251View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0uxr-1029000000-ea43e68bb4fffc9657b1View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-9121000000-cce64d1dcf28012d72f8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0006-9520000000-d95a37794c98d95dd2b0View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014i-2097000000-1f5b8c8eefe1a491d0c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0bt9-9060000000-7550c32b4e1dfcbc4593View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9020000000-5cbe1fbb421cacd42e98View in MoNA
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Feces
Tissue Location
  • Epidermis
  • Stratum Corneum
  • Thyroid Gland
PathwaysNot Available
NameSMPDB/PathwhizKEGG
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Colorectal cancer
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB023381
KNApSAcK IDNot Available
Chemspider ID108921
KEGG Compound IDC12144
BioCyc IDPHYTOSPINGOSINE
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN ID7066
PubChem Compound122121
PDB IDNot Available
ChEBI ID46961
References
Synthesis ReferenceMulzer, 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)Download (PDF)
General References
  1. Flamand N, Justine P, Bernaud F, Rougier A, Gaetani Q: In vivo distribution of free long-chain sphingoid bases in the human stratum corneum by high-performance liquid chromatographic analysis of strippings. J Chromatogr B Biomed Appl. 1994 Jun 3;656(1):65-71. [PubMed:7952048 ]
  2. Bouchon B, Portoukalian J, Orgiazzi J, Bornet H: Selective enrichment of phytosphingosine in glycosphingolipids of isolated human thyrocytes as compared to the whole thyroid. Biochem Biophys Res Commun. 1987 Mar 30;143(3):827-31. [PubMed:3566758 ]
  3. 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. [PubMed:8046331 ]
  4. Madison KC, Swartzendruber DC, Wertz PW, Downing DT: Sphingolipid metabolism in organotypic mouse keratinocyte cultures. J Invest Dermatol. 1990 Dec;95(6):657-64. [PubMed:2123494 ]
  5. 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. [PubMed:8048941 ]
  6. Nenoff P, Haustein UF: In vitro activity of phytosphingosines against Malassezia furfur and Candida albicans. Acta Derm Venereol. 2002;82(3):170-3. [PubMed:12353705 ]
  7. 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. [PubMed:12531554 ]
  8. 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. [PubMed:8706124 ]
  9. 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. [PubMed:12576463 ]

Only showing the first 10 proteins. There are 44 proteins in total.

Enzymes

General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGP
Uniprot ID:
P57054
Molecular weight:
18089.055
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGC
Uniprot ID:
Q92535
Molecular weight:
33582.18
General function:
Involved in lipid metabolic process
Specific function:
Hydrolyzes the sphingolipid ceramide into sphingosine and free fatty acid.
Gene Name:
ASAH1
Uniprot ID:
Q13510
Molecular weight:
44045.27
General function:
Involved in sphingolipid activator protein activity
Specific function:
Binds gangliosides and stimulates ganglioside GM2 degradation. It stimulates only the breakdown of ganglioside GM2 and glycolipid GA2 by beta-hexosaminidase A. It extracts single GM2 molecules from membranes and presents them in soluble form to beta-hexosaminidase A for cleavage of N-acetyl-D-galactosamine and conversion to GM3
Gene Name:
GM2A
Uniprot ID:
P17900
Molecular weight:
20838.1
General function:
Involved in immune response
Specific function:
T-cell surface glycoprotein CD1e, soluble is required for the presentation of glycolipid antigens on the cell surface. The membrane-associated form is not active
Gene Name:
CD1E
Uniprot ID:
P15812
Molecular weight:
43626.1

Only showing the first 10 proteins. There are 44 proteins in total.