Cannabis Compound Database: Showing Compound Card for Phytosphingosine (CDB004970)

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Identification Taxonomy Ontology Physical properties Spectra Protein target Pathways Concentrations Links References enzymes (32)transporters (7) Show 39 proteins XML

Record Information

Version

1.0

Created at

2020-04-17 18:55:47 UTC

Updated at

2020-12-07 19:11:23 UTC

CannabisDB ID

CDB004970

Secondary Accession Numbers

Not Available

Cannabis Compound 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. Phytosphingosine is a sphingoid base, a fundamental building block of more complex sphingolipids. Phytosphingosine is expected to be in Cannabis as all living plants are known to produce and metabolize it.

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

317.51

Monoisotopic Molecular Weight

317.293

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

Disposition

Source:

Biological location:

Tissue and substructures:

Organ and components:

Endocrine gland:

Thyroid gland

Cell and elements:

Extracellular

Subcellular:

Role

Industrial application:

Biological role:

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	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

EI-MS/GC-MS

Type	Description	Splash Key	View
GC-MS	Phytosphingosine, non-derivatized, GC-MS Spectrum	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	Spectrum
GC-MS	Phytosphingosine, non-derivatized, GC-MS Spectrum	splash10-0udi-0590000000-55f1259ff17447451d03	Spectrum
GC-MS	Phytosphingosine, non-derivatized, GC-MS Spectrum	splash10-001i-1910000000-6a156f8b67eb8d2e2af8	Spectrum
GC-MS	Phytosphingosine, non-derivatized, GC-MS Spectrum	splash10-0udi-0590000000-55f1259ff17447451d03	Spectrum
Predicted GC-MS	Phytosphingosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	splash10-08fu-9240000000-f0c822bc0197665bc676	Spectrum
Predicted GC-MS	Phytosphingosine, 3 TMS, Predicted GC-MS Spectrum - 70eV, Positive	splash10-0pxr-8498250000-59c3446ba7cde2700251	Spectrum
Predicted GC-MS	Phytosphingosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum
Predicted GC-MS	Phytosphingosine, non-derivatized, Predicted GC-MS Spectrum - 70eV, Positive	Not Available	Spectrum

MS/MS

Type	Description	Splash Key	View
MS/MS	LC-MS/MS Spectrum - LC-ESI-QFT , positive	splash10-03di-9025000000-41591a03203ebe6783ab	2020-07-21	View Spectrum
MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF 35V, positive	splash10-03yi-9055000000-c534f58f04d1f008079f	2020-07-21	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-014i-0009000000-2467642b22875f4e99a1	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-014i-0009000000-94b30bf1ae7ab25e566e	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-03xr-9037000000-2e7ea43f8d534e10f1d4	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 15V, positive	splash10-03di-9020000000-ac9c04a9082abb540f22	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 19V, positive	splash10-03di-9010000000-e1fe657c8693bf3f19e7	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 26V, positive	splash10-03di-9000000000-f71f3038d0b8478d679c	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 31V, positive	splash10-03di-9000000000-795a4947f722e8f61620	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 38V, positive	splash10-03di-9000000000-e62d8c5bcb55aa166603	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 44V, positive	splash10-03di-9000000000-cb05f289ecdcd16de4e7	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 52V, positive	splash10-03di-9000000000-e898ac84341e318b5862	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 60V, positive	splash10-08fr-9000000000-b048fe168eacee259394	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - Orbitrap 72V, positive	splash10-0900-9000000000-d72ddb3ba2da45266fab	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0udi-0039000000-33d42068332d814a2c83	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-06yt-6940000000-fdeb46044349d9fcc996	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0006-9000000000-981a59d4f1dd5e03c5ac	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-0ik9-0190000000-d31bcfd06b73972a4300	2020-07-22	View Spectrum
MS/MS	LC-MS/MS Spectrum - n/a 22V, positive	splash10-03di-2290000000-b7855c3c2203ca25bab3	2020-07-22	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0uxr-1029000000-ea43e68bb4fffc9657b1	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dl-9121000000-cce64d1dcf28012d72f8	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9520000000-d95a37794c98d95dd2b0	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014i-2097000000-1f5b8c8eefe1a491d0c9	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0bt9-9060000000-7550c32b4e1dfcbc4593	2016-09-12	View Spectrum
Predicted MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9020000000-5cbe1fbb421cacd42e98	2016-09-12	View Spectrum

NMR

Not Available

Pathways

Not Available

Protein Targets

Enzymes

Protein Name	Gene Name	Locus	Uniprot ID	Details
Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	GBGT1	9q34.13-q34.3	Q8N5D6	details
N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase	PIGL	17p12-p11.2	Q9Y2B2	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q	PIGQ	16p13.3	Q9BRB3	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit A	PIGA	Xp22.1	P37287	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit H	PIGH	14q24.1	Q14442	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit P	PIGP	21q22.2	P57054	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit C	PIGC	1q23-q25	Q92535	details
Acid ceramidase	ASAH1	8p22	Q13510	details
Ganglioside GM2 activator	GM2A	5q33.1	P17900	details
T-cell surface glycoprotein CD1e, membrane-associated	CD1E	1q22-q23	P15812	details
Epididymal secretory protein E1	NPC2	14q24.3	P61916	details
Antigen-presenting glycoprotein CD1d	CD1D	1q22-q23	P15813	details
GPI mannosyltransferase 1	PIGM	1q23.2	Q9H3S5	details
Phosphatidylinositol-glycan biosynthesis class W protein	PIGW		Q7Z7B1	details
Phosphatidylinositol-glycan biosynthesis class X protein	PIGX	3q29	Q8TBF5	details
GPI mannosyltransferase 4	PIGZ	3q29	Q86VD9	details
Lactosylceramide 1,3-N-acetyl-beta-D-glucosaminyltransferase	B3GNT5	3q28	Q9BYG0	details
Beta-1,3-galactosyltransferase 5	B3GALT5	21q22.3	Q9Y2C3	details
GPI mannosyltransferase 3	PIGB	15q21-q22	Q92521	details
Phosphatidylinositol-glycan biosynthesis class F protein	PIGF	2p21-p16	Q07326	details
GPI ethanolamine phosphate transferase 2	PIGG	4p16.3	Q5H8A4	details
GPI ethanolamine phosphate transferase 1	PIGN	18q21.33	O95427	details
GPI ethanolamine phosphate transferase 3	PIGO	9p13.3	Q8TEQ8	details
GPI transamidase component PIG-S	PIGS	17p13.2	Q96S52	details
GPI transamidase component PIG-T	PIGT	20q12-q13.12	Q969N2	details
Phosphatidylinositol glycan anchor biosynthesis class U protein	PIGU	20q11.22	Q9H490	details
GPI mannosyltransferase 2	PIGV	1p36.11	Q9NUD9	details
Phosphatidylinositol N-acetylglucosaminyltransferase subunit Y	PIGY	4q22.1	Q3MUY2	details
Alkaline ceramidase 2	ACER2	9p22.1	Q5QJU3	details
Non-lysosomal glucosylceramidase	GBA2	9p13.3	Q9HCG7	details
Alkaline ceramidase 1	ACER1	19p13.3	Q8TDN7	details
GPI-anchor transamidase	PIGK	1p31.1	Q92643	details

Transporters

Protein Name	Gene Name	Locus	Uniprot ID	Details
Pleckstrin homology domain-containing family A member 8	PLEKHA8	7p21-p11.2	Q96JA3	details
Protein PLEKHA9	PLEKHA9	12q	O95397	details
Glycolipid transfer protein domain-containing protein 2	GLTPD2	17p13.2	A6NH11	details
Putative uncharacterized protein PLEKHA8	PLEKHA8	7p21-p11.2	B5MDU3	details
Glycolipid transfer protein domain-containing protein 1	GLTPD1	1p36.33	Q5TA50	details
Putative uncharacterized protein DKFZp434L0435	DKFZp434L0435		Q9UFH6	details
Glycolipid transfer protein	GLTP	12q24.11	Q9NZD2	details

Metal Bindings

Not Available

Receptors

Not Available

Transcriptional Factors

Not Available

Concentrations Data

Not Available

External Links

HMDB ID

HMDB0004610

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB 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

General References

Not Available

Only showing the first 10 proteins. There are 39 proteins in total.

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Enzymes

Enzyme Details

1. Globoside alpha-1,3-N-acetylgalactosaminyltransferase 1

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

Enzyme Details

2. N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase

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

Enzyme Details

3. Phosphatidylinositol N-acetylglucosaminyltransferase subunit Q

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

Enzyme Details

4. Phosphatidylinositol N-acetylglucosaminyltransferase subunit A

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

Enzyme Details

5. Phosphatidylinositol N-acetylglucosaminyltransferase subunit H

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

Enzyme Details

6. Phosphatidylinositol N-acetylglucosaminyltransferase subunit P

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

Enzyme Details

7. Phosphatidylinositol N-acetylglucosaminyltransferase subunit C

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

Enzyme Details

8. Acid ceramidase

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

Enzyme Details

9. Ganglioside GM2 activator

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

Enzyme Details

10. T-cell surface glycoprotein CD1e, membrane-associated

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

Transporters

Enzyme Details

1. Pleckstrin homology domain-containing family A member 8

General function:: Involved in glycolipid transporter activity
Specific function:: Involved in TGN-to-plasma membrane transport and in the formation of post-Golgi constitutive carriers. May play a role in ensuring the coordination of the budding and the fission reactions
Gene Name:: PLEKHA8
Uniprot ID:: Q96JA3
Molecular weight:: 58306.0

Enzyme Details

2. Protein PLEKHA9

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: PLEKHA9
Uniprot ID:: O95397
Molecular weight:: 43538.3

Enzyme Details

3. Glycolipid transfer protein domain-containing protein 2

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: GLTPD2
Uniprot ID:: A6NH11
Molecular weight:: 31641.2

Enzyme Details

4. Putative uncharacterized protein PLEKHA8

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: PLEKHA8
Uniprot ID:: B5MDU3
Molecular weight:: 49308.8

Enzyme Details

5. Glycolipid transfer protein domain-containing protein 1

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: GLTPD1
Uniprot ID:: Q5TA50
Molecular weight:: 24364.8

Enzyme Details

6. Putative uncharacterized protein DKFZp434L0435

General function:: Involved in glycolipid transporter activity
Specific function:: Not Available
Gene Name:: DKFZp434L0435
Uniprot ID:: Q9UFH6
Molecular weight:: 6175.1

Enzyme Details

7. Glycolipid transfer protein

General function:: Involved in glycolipid transporter activity
Specific function:: Accelerates the intermembrane transfer of various glycolipids. Catalyzes the transfer of various glycosphingolipids between membranes but does not catalyze the transfer of phospholipids. May be involved in the intracellular translocation of glucosylceramides
Gene Name:: GLTP
Uniprot ID:: Q9NZD2
Molecular weight:: 23849.6

Only showing the first 10 proteins. There are 39 proteins in total.

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Showing Compound Card for Phytosphingosine (CDB004970)

Structure for CDB004970 (Phytosphingosine)

Enzymes

Transporters