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3-Dehydrosphinganine (YMDB00183)

Identification
YMDB IDYMDB00183
Name3-Dehydrosphinganine
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
Description3-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
Thumb
MOLSDFPDBSMILESInChI
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 number16105-69-4
WeightAverage: 299.4919
Monoisotopic: 299.282429433
InChI KeyKBUNOSOGGAARKZ-KRWDZBQOSA-N
InChIInChI=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 Name3-ketosphinganine
Chemical FormulaC18H37NO2
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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentBeta-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 FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.0013 g/LALOGPS
logP5.45ALOGPS
logP5.18ChemAxon
logS-5.4ALOGPS
pKa (Strongest Acidic)14.38ChemAxon
pKa (Strongest Basic)7.54ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area63.32 ŲChemAxon
Rotatable Bond Count16ChemAxon
Refractivity90.03 m³·mol⁻¹ChemAxon
Polarizability39.56 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • endoplasmic reticulum
Organoleptic PropertiesNot Available
SMPDB Pathways
Biosynthesis of unsaturated fatty acidsPW002403 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (docosanoyl)PW002408 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (icosanoyl)PW002434 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (stearoyl)PW002435 ThumbThumb?image type=greyscaleThumb?image type=simple
Biosynthesis of unsaturated fatty acids (tetracosanoyl-CoA)PW002404 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Biosynthesis of unsaturated fatty acidsec01040 Map01040
Sphingolipid metabolismec00600 Map00600
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 ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01p9-9120000000-135052b999433b5dd30bJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03di-9321000000-e0d96cb3bea3c320412aJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f89-2096000000-8323a157b44b31f2331aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01qa-4491000000-39be7a6025f78d062cb5JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ox-9510000000-a675e52903f069501f67JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1090000000-e36f44a44812cc09023cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-015j-4090000000-4a24200105a7fd0afd1eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9020000000-edd2ec1e7a7fae113d2fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-3069000000-e43a689cbba7742dc5c6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01q9-9282000000-f83e19a33602a8a25cb8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-9000000000-f16a410d8c3330af51f2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014j-0090000000-7d1c46d2460baf58b0dcJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ej-3090000000-b775508a0489f38a77f7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9010000000-b10c9eb2adca17092c8cJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
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:
ResourceLink
CHEBI ID17862
HMDB IDHMDB01480
Pubchem Compound ID631
Kegg IDC02934
ChemSpider ID388895
FOODB IDFDB022645
Wikipedia IDNot Available
BioCyc IDDEHYDROSPHINGANINE

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.