MiMeDB: Showing metabocard for Phytosphingosine (MMDBc0000605)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2020-12-10 18:50:57 UTC

Update Date

2024-10-09 23:50:50 UTC

Metabolite ID

MMDBc0000605

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 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

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

Molecular Formula

C₁₈H₃₉NO₃

Average Mass

317.5072

Monoisotopic Mass

317.292994119

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

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 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Extracellular
Membrane

Biospecimen Locations

Epidermis
Feces
Placenta
Thyroid Gland

Tissue Locations

Epidermis
Placenta
Thyroid Gland

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species
MMDBp0192100	Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	Unknown	Q8N5D6	Homo sapiens
MMDBp0192203	N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase	Enzyme	Q9Y2B2	Homo sapiens
MMDBp0192558	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q	Enzyme	Q9BRB3	Homo sapiens
MMDBp0192559	Phosphatidylinositol N-acetylglucosaminyltransferase subunit A	Enzyme	P37287	Homo sapiens
MMDBp0192560	Phosphatidylinositol N-acetylglucosaminyltransferase subunit H	Enzyme	Q14442	Homo sapiens
MMDBp0192561	Phosphatidylinositol N-acetylglucosaminyltransferase subunit P	Enzyme	P57054	Homo sapiens
MMDBp0192562	Phosphatidylinositol N-acetylglucosaminyltransferase subunit C	Enzyme	Q92535	Homo sapiens
MMDBp0192690	Acid ceramidase	Enzyme	Q13510	Homo sapiens
MMDBp0193223	Ganglioside GM2 activator	Enzyme	P17900	Homo sapiens
MMDBp0193531	T-cell surface glycoprotein CD1e, membrane-associated	Enzyme	P15812	Homo sapiens
MMDBp0193636	Epididymal secretory protein E1	Enzyme	P61916	Homo sapiens
MMDBp0193673	Antigen-presenting glycoprotein CD1d	Enzyme	P15813	Homo sapiens
MMDBp0193742	GPI mannosyltransferase 1	Enzyme	Q9H3S5	Homo sapiens
MMDBp0193755	Phosphatidylinositol-glycan biosynthesis class W protein	Enzyme	Q7Z7B1	Homo sapiens
MMDBp0193805	Phosphatidylinositol-glycan biosynthesis class X protein	Enzyme	Q8TBF5	Homo sapiens
MMDBp0193806	GPI mannosyltransferase 4	Enzyme	Q86VD9	Homo sapiens
MMDBp0194033	Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase	Enzyme	Q9BYG0	Homo sapiens
MMDBp0194044	Beta-1,3-galactosyltransferase 5	Enzyme	Q9Y2C3	Homo sapiens
MMDBp0194119	GPI mannosyltransferase 3	Enzyme	Q92521	Homo sapiens
MMDBp0194120	Phosphatidylinositol-glycan biosynthesis class F protein	Enzyme	Q07326	Homo sapiens
MMDBp0194121	GPI ethanolamine phosphate transferase 2	Enzyme	Q5H8A4	Homo sapiens
MMDBp0194122	GPI ethanolamine phosphate transferase 1	Enzyme	O95427	Homo sapiens
MMDBp0194123	GPI ethanolamine phosphate transferase 3	Enzyme	Q8TEQ8	Homo sapiens
MMDBp0194124	GPI transamidase component PIG-S	Enzyme	Q96S52	Homo sapiens
MMDBp0194125	GPI transamidase component PIG-T	Enzyme	Q969N2	Homo sapiens
MMDBp0194126	Phosphatidylinositol glycan anchor biosynthesis class U protein	Enzyme	Q9H490	Homo sapiens
MMDBp0194127	GPI mannosyltransferase 2	Enzyme	Q9NUD9	Homo sapiens
MMDBp0194128	Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y	Enzyme	Q3MUY2	Homo sapiens
MMDBp0194133	Pleckstrin homology domain-containing family A member 8	Unknown	Q96JA3	Homo sapiens
MMDBp0195880	Alkaline ceramidase 2	Enzyme	Q5QJU3	Homo sapiens
MMDBp0195885	Non-lysosomal glucosylceramidase	Enzyme	Q9HCG7	Homo sapiens
MMDBp0196227	Alkaline ceramidase 1	Enzyme	Q8TDN7	Homo sapiens
MMDBp0196528	GPI-anchor transamidase	Enzyme	Q92643	Homo sapiens
MMDBp0196556	Glycosylphosphatidylinositol anchor attachment 1 protein	Unknown	O43292	Homo sapiens
MMDBp0196557	Protein PLEKHA9	Unknown	O95397	Homo sapiens
MMDBp0196558	Glycolipid transfer protein domain-containing protein 2	Unknown	A6NH11	Homo sapiens
MMDBp0196559	Putative uncharacterized protein PLEKHA8	Unknown	B5MDU3	Homo sapiens
MMDBp0196560	T-cell surface glycoprotein CD1a	Unknown	P06126	Homo sapiens
MMDBp0196561	Glycolipid transfer protein domain-containing protein 1	Unknown	Q5TA50	Homo sapiens
MMDBp0196562	T-cell surface glycoprotein CD1c	Unknown	P29017	Homo sapiens
MMDBp0196563	Lipopolysaccharide-binding protein	Unknown	P18428	Homo sapiens
MMDBp0196564	Putative uncharacterized protein DKFZp434L0435	Unknown	Q9UFH6	Homo sapiens
MMDBp0196565	T-cell surface glycoprotein CD1b	Unknown	P29016	Homo sapiens
MMDBp0196566	Glycolipid transfer protein	Unknown	Q9NZD2	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0009101	Phytosphingosine	Phytosphingosine 1-phosphate	sphingosine kinase 1		VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Verrucomicrobia	1	Human feces; Human stool; Human ; Human urine	Indirect association between microbiota composition and metabolites measured in host biospecimen
Bacteria	Firmicutes	4	Human feces; Human stool; Human ; Human urine; Human sputum	Indirect association between microbiota composition and metabolites measured in host biospecimen
Archaea	Euryarchaeota	1	Human feces; Human	Indirect association between microbiota composition and metabolites measured in host biospecimen
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified				HMDB
Human Epidermis	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Placenta	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Thyroid gland	Detected but not Quantified	Not Specified	Not Specified	Normal	HMDB	34986597
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	27543620
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	25037050
Human Feces	Detected but not Quantified	Adult (>18 years old)	Both	Normal	HMDB	29808030

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

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Madison KC, Swartzendruber DC, Wertz PW, Downing DT: Sphingolipid metabolism in organotypic mouse keratinocyte cultures. J Invest Dermatol. 1990 Dec;95(6):657-64. doi: 10.1111/1523-1747.ep12514333. [PubMed:2123494 ]
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. doi: 10.1016/0006-291x(87)90323-8. [PubMed:3566758 ]
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. doi: 10.1016/0378-4347(94)80021-9. [PubMed:7952048 ]
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. doi: 10.1084/jem.180.2.525. [PubMed: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. doi: 10.1006/bbrc.1994.1988. [PubMed: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. doi: 10.1016/s0092-8674(00)80091-4. [PubMed:8706124 ]
Nenoff P, Haustein UF: In vitro activity of phytosphingosines against Malassezia furfur and Candida albicans. Acta Derm Venereol. 2002;82(3):170-3. doi: 10.1080/00015550260132433. [PubMed:12353705 ]
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. doi: 10.1016/s1388-1981(02)00341-4. [PubMed:12531554 ]
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 ]
Elshenawy S, Pinney SE, Stuart T, Doulias PT, Zura G, Parry S, Elovitz MA, Bennett MJ, Bansal A, Strauss JF 3rd, Ischiropoulos H, Simmons RA: The Metabolomic Signature of the Placenta in Spontaneous Preterm Birth. Int J Mol Sci. 2020 Feb 4;21(3). pii: ijms21031043. doi: 10.3390/ijms21031043. [PubMed:32033212 ]

Showing metabocard for Phytosphingosine (MMDBc0000605)

MOL for #<Metabolite:0x00007f46c6dc4ee8>

3D MOL for #<Metabolite:0x00007f46c6dc4ee8>

3D SDF for #<Metabolite:0x00007f46c6dc4ee8>

3D-SDF for #<Metabolite:0x00007f46c6dc4ee8>

PDB for #<Metabolite:0x00007f46c6dc4ee8>

3D PDB for #<Metabolite:0x00007f46c6dc4ee8>

SMILES for #<Metabolite:0x00007f46c6dc4ee8>

INCHI for #<Metabolite:0x00007f46c6dc4ee8>

Structure for #<Metabolite:0x00007f46c6dc4ee8>

3D Structure for #<Metabolite:0x00007f46c6dc4ee8>