Hmdb loader
Show more...Show more...Show more...Show more...
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2006-08-13 22:13:39 UTC
Update Date2022-09-22 18:34:18 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-PhytosphingenineHMDB
(2S,3S,4R)-2-Amino-1,3,4-octadecanetriolHMDB
(2S,3S,4R)-2-Amino-1,3,4-trihydroxyoctadecaneHMDB
D-Ribo-phytosphingosineHMDB
SP(t18:0)HMDB
PhytosphingosineHMDB
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
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.
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
Physiological effectNot Available
Disposition
Biological locationSource
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point102 - 103 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-MetCCS_train_neg180.68230932474
[M+H]+MetCCS_train_pos196.24630932474
[M-H]-Not Available180.682http://allccs.zhulab.cn/database/detail?ID=AllCCS00000425
[M+H]+Not Available196.794http://allccs.zhulab.cn/database/detail?ID=AllCCS00000425
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue Locations
  • Epidermis
  • Placenta
  • Thyroid Gland
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal
details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodExpected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer
details
UrineDetected but not QuantifiedNot QuantifiedNot SpecifiedNot SpecifiedCancer patients undergoing total body irradiation details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023381
KNApSAcK IDNot Available
Chemspider ID108921
KEGG Compound IDC12144
BioCyc IDPHYTOSPINGOSINE
BiGG IDNot Available
Wikipedia LinkPhytosphingosine
METLIN ID7066
PubChem Compound122121
PDB IDNot Available
ChEBI ID46961
Food Biomarker OntologyNot Available
VMH IDM02749
MarkerDB IDNot Available
Good Scents IDNot Available
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)Not Available
General References

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.