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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
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-DehydrosphinganineNADP + Sphinganine
Palmityl-CoA + L-Serine + hydron Coenzyme A + Carbon dioxide + 3-Dehydrosphinganine
Palmityl-CoA + L-Serine3-Dehydrosphinganine + Carbon dioxide
Sphinganine + NADPH3-Dehydrosphinganine + NADP
KEGG Reactions
3-Dehydrosphinganine + NADPH + hydronSphinganine + NADP
Palmityl-CoA + L-Serine3-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 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
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

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).
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).
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.