3-Dehydrosphinganine (YMDB00183)

Identification

YMDB ID

YMDB00183

Name

3-Dehydrosphinganine

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

3-Dehydrosphinganine 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

(2S)-2-amino-1-hydroxyoctadecan-3-one
1-Hydroxy-2-amino-3-oxo-octadecane
2-amino-1-hydroxy-3-Octadecanone
3-Dehydro-D-sphinganine
3-dehydrosphinganine
3-ketodihydrosphingosine
3-Ketosphinganine
KDHS
Ketodihydrosphingosine
(+-)-Isomer OF ketodihydrosphingosine
(S)-Isomer OF ketodihydrosphingosine

CAS number

16105-69-4

Weight

Average: 299.4919
Monoisotopic: 299.282429433

InChI Key

KBUNOSOGGAARKZ-KRWDZBQOSA-N

InChI

InChI=1S/C18H37NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-18(21)17(19)16-20/h17,20H,2-16,19H2,1H3/t17-/m0/s1

IUPAC Name

(2S)-2-amino-1-hydroxyoctadecan-3-one

Traditional IUPAC Name

3-ketosphinganine

Chemical Formula

C₁₈H₃₇NO₂

SMILES

[H]OC([H])([H])[C@]([H])(N([H])[H])C(=O)C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])C([H])([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as beta-hydroxy ketones. These are ketones containing a hydroxyl group attached to the beta-carbon atom, relative to the C=O group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Beta-hydroxy ketones

Alternative Parents

Substituents

Beta-hydroxy ketone
Alpha-aminoketone
Organic nitrogen compound
Organopnictogen compound
Organic oxide
Hydrocarbon derivative
Primary amine
Primary alcohol
Organonitrogen compound
Primary aliphatic amine
Amine
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

2-amino-1-hydroxyoctadecan-3-one (CHEBI:17862 )
Sphing-4-enines (Sphingosines) (C02934 )
Sphinganines (LMSP01020002 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

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

Predicted Properties

Property	Value	Source
Water Solubility	0.0013 g/L	ALOGPS
logP	5.45	ALOGPS
logP	5.18	ChemAxon
logS	-5.4	ALOGPS
pKa (Strongest Acidic)	14.38	ChemAxon
pKa (Strongest Basic)	7.54	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	63.32 Å²	ChemAxon
Rotatable Bond Count	16	ChemAxon
Refractivity	90.03 m³·mol⁻¹	ChemAxon
Polarizability	39.56 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	0	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

endoplasmic reticulum

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

hydron + NADPH + 3-Dehydrosphinganine → NADP + Sphinganine

Palmityl-CoA + L-Serine + hydron Coenzyme A + Carbon dioxide + 3-Dehydrosphinganine

Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxide

Sphinganine + NADPH → 3-Dehydrosphinganine + NADP

KEGG Reactions

3-Dehydrosphinganine + NADPH + hydron ↔ Sphinganine + NADP

Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxide + Coenzyme A

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-01p9-9120000000-135052b999433b5dd30b	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positive	splash10-03di-9321000000-e0d96cb3bea3c320412a	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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0f89-2096000000-8323a157b44b31f2331a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01qa-4491000000-39be7a6025f78d062cb5	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-01ox-9510000000-a675e52903f069501f67	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-1090000000-e36f44a44812cc09023c	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-015j-4090000000-4a24200105a7fd0afd1e	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-052f-9020000000-edd2ec1e7a7fae113d2f	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-3069000000-e43a689cbba7742dc5c6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-01q9-9282000000-f83e19a33602a8a25cb8	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4l-9000000000-f16a410d8c3330af51f2	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-014j-0090000000-7d1c46d2460baf58b0dc	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-06ej-3090000000-b775508a0489f38a77f7	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a4l-9010000000-b10c9eb2adca17092c8c	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:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Obeid, L. M., Okamoto, Y., Mao, C. (2002). "Yeast sphingolipids: metabolism and biology." Biochim Biophys Acta 1585:163-171.12531550

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	17862
HMDB ID	HMDB01480
Pubchem Compound ID	631
Kegg ID	C02934
ChemSpider ID	388895
FOODB ID	FDB022645
Wikipedia ID	Not Available
BioCyc ID	DEHYDROSPHINGANINE

Enzymes

Protein Details

1. Serine palmitoyltransferase 1

General function:: Involved in transferase activity, transferring nitrogenous groups
Specific function:: Component of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
Gene Name:: LCB1
Uniprot ID:: P25045
Molecular weight:: 62206.60156

Reactions

Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2).

Protein Details

2. Serine palmitoyltransferase 2

General function:: Involved in transferase activity
Specific function:: Catalytic subunit of serine palmitoyltransferase (SPT), which catalyzes the committed step in the synthesis of sphingolipids, the condensation of serine with palmitoyl CoA to form the long chain base 3-ketosphinganine
Gene Name:: LCB2
Uniprot ID:: P40970
Molecular weight:: 63110.19922

Reactions

Palmitoyl-CoA + L-serine → CoA + 3-dehydro-D-sphinganine + CO(2).

Protein Details

3. 3-ketodihydrosphingosine reductase TSC10

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS)
Gene Name:: TSC10
Uniprot ID:: P38342
Molecular weight:: 35986.19922

Reactions

Sphinganine + NADP(+) → 3-dehydrosphinganine + NADPH.

Structure for #<Compound:0xb180c788>

Enzymes

Reactions

Reactions

Reactions