4-Hydroxysphinganine (YMDB01101)

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Identification

YMDB ID

YMDB01101

Name

4-Hydroxysphinganine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

Phytosphingosine (4-hydroxysphinganine) is an intermediate in sphingolipid metabolism pathway. Sphingolipids are essential components of the plasma membrane in all eukaryotic cells. S. cerevisiae cells make three complex sphingolipids: inositol-phosphoceramide (IPC), mannose-inositol-phosphoceramide (MIPC), and mannosyl-diinositol-phosphorylceramide (M(IP)2C). Sphingolipid long chain bases (LCBs) - dihydrosphingosine (DHS) and phytosphingosine (PHS) - are implicated as secondary messengers in vital signaling pathways. [Biocyc SPHINGOLIPID-SYN-PWY]

Structure

MOL SDF PDB SMILES InChI

Synonyms

(+)-D-ribo-Phytosphingosine
[2S-(2R*,3R*,4S*)]-2-amino-1,3,4-Octadecanetriol
4-D-hydroxy-Sphinganine
4-D-Hydroxysphinganine
4D-Hydroxysphinganine
C18-Phytosphingosine
Ceramide II
D-ribo-1,3,4-Trihydroxy-2-aminooctadecane
D-ribo-2-amino-1,3,4-Octadecanetriol
Kohlenstoff
N-Acyl-4-hydroxysphinganine
Phytoceramide
Phytosphingosine
4-R-Hydroxyoctadecasphinganine
8-(Z-e)-C18-Phytosphingenine
(2S,3S,4R)-2-Amino-1,3,4-octadecanetriol
(2S,3S,4R)-2-Amino-1,3,4-trihydroxyoctadecane
D-Ribo-phytosphingosine
SP(t18:0)

CAS number

554-62-1

Weight

Average: 317.5072
Monoisotopic: 317.292994119

InChI Key

AERBNCYCJBRYDG-KSZLIROESA-N

InChI

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

IUPAC Name

(2S,3S,4R)-2-aminooctadecane-1,3,4-triol

Traditional IUPAC Name

phytosphingosine

Chemical Formula

C₁₈H₃₉NO₃

SMILES

[H][C@](N)(CO)[C@]([H])(O)[C@H](O)CCCCCCCCCCCCCC

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 )

Physical Properties

State

Solid

Charge

Melting point

102-103 °C

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	0.045 g/L	ALOGPS
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	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

Not Available

Organoleptic Properties

Not Available

SMPDB Pathways

Biosynthesis of unsaturated fatty acids	PW002403
Biosynthesis of unsaturated fatty acids (docosanoyl)	PW002408
Biosynthesis of unsaturated fatty acids (icosanoyl)	PW002434
Biosynthesis of unsaturated fatty acids (stearoyl)	PW002435
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)	PW002404

KEGG Pathways

Biosynthesis of unsaturated fatty acids	ec01040
Sphingolipid metabolism	ec00600

SMPDB Reactions

Not Available

KEGG Reactions

Not Available

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

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

References

References:

Ejsing, C. S., Sampaio, J. L., Surendranath, V., Duchoslav, E., Ekroos, K., Klemm, R. W., Simons, K., Shevchenko, A. (2009). "Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry." Proc Natl Acad Sci U S A 106:2136-2141.19174513

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	46961
HMDB ID	HMDB04610
Pubchem Compound ID	122121
Kegg ID	C12144
ChemSpider ID	108921
FOODB ID	FDB023381
Wikipedia ID	Phytosphingosine
BioCyc ID	PHYTOSPINGOSINE

Structure for #<Compound:0x95c4c0e4>