Showing metabocard for 3-Dehydrosphinganine (BMDB0001480)

IdentificationTaxonomyPhysical propertiesPathwaysSpectraConcentrationsLinksReferencesenzymes (3) Show 3 proteinsXML
Record Information
Version1.0
Creation Date2016-09-30 22:46:31 UTC
Update Date2020-05-21 16:28:58 UTC
BMDB IDBMDB0001480
Secondary Accession Numbers
  • BMDB01480
Metabolite Identification
Common Name3-Dehydrosphinganine
Description3-Dehydrosphinganine, also known as KDHS or ketodihydrosphingosine, 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. Thus, 3-dehydrosphinganine is considered to be a sphingoid base lipid molecule. 3-Dehydrosphinganine is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral. 3-Dehydrosphinganine exists in all eukaryotes, ranging from yeast to humans.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
3-Dehydro-D-sphinganineChEBI
3-KetodihydrosphingosineChEBI
3-KetosphinganineChEBI
(2S)-2-Amino-1-hydroxyoctadecan-3-oneHMDB
1-Hydroxy-2-amino-3-oxo-octadecaneHMDB
2-Amino-1-hydroxy-3-octadecanoneHMDB
KDHSHMDB
KetodihydrosphingosineHMDB
(+-)-Isomer OF ketodihydrosphingosineHMDB
(S)-Isomer OF ketodihydrosphingosineHMDB
Chemical FormulaC18H37NO2
Average Molecular Weight299.4919
Monoisotopic Molecular Weight299.282429433
IUPAC Name(2S)-2-amino-1-hydroxyoctadecan-3-one
Traditional Name3-ketosphinganine
CAS Registry Number16105-69-4
SMILES
CCCCCCCCCCCCCCCC(=O)[C@@H](N)CO
InChI Identifier
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
InChI KeyKBUNOSOGGAARKZ-KRWDZBQOSA-N
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
Ontology
StatusExpected but not Quantified
Origin
  • Endogenous
  • Exogenous
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Cell membrane
  • Cytoplasm
  • Membrane
  • Mitochondria
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
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
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01p9-9120000000-135052b999433b5dd30bView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03di-9321000000-e0d96cb3bea3c320412aView in MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f89-2096000000-8323a157b44b31f2331aView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01qa-4491000000-39be7a6025f78d062cb5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ox-9510000000-a675e52903f069501f67View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1090000000-e36f44a44812cc09023cView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-015j-4090000000-4a24200105a7fd0afd1eView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9020000000-edd2ec1e7a7fae113d2fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0ue9-3069000000-e43a689cbba7742dc5c6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01q9-9282000000-f83e19a33602a8a25cb8View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4l-9000000000-f16a410d8c3330af51f2View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-014j-0090000000-7d1c46d2460baf58b0dcView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ej-3090000000-b775508a0489f38a77f7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9010000000-b10c9eb2adca17092c8cView in MoNA
1D NMR13C NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 100 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 1000 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 200 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 300 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 400 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 500 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 600 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 700 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 800 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR13C NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
1D NMR1H NMR Spectrum (1D, 900 MHz, H2O, predicted)Not AvailableView in JSpectraViewer
Biological Properties
Cellular Locations
  • Cell membrane
  • Cytoplasm
  • Membrane
  • Mitochondria
Biospecimen LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
HMDB IDHMDB0001480
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB022645
KNApSAcK IDNot Available
Chemspider ID388895
KEGG Compound IDC02934
BioCyc IDDEHYDROSPHINGANINE
BiGG ID1453300
Wikipedia LinkNot Available
METLIN ID3428
PubChem Compound439853
PDB IDNot Available
ChEBI ID17862
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. 3-ketodihydrosphingosine reductase
General function:
Lipid transport and metabolism
Specific function:
Catalyzes the reduction of 3-ketodihydrosphingosine (KDS) to dihydrosphingosine (DHS).
Gene Name:
KDSR
Uniprot ID:
Q2KIJ5
Molecular weight:
36020.0
Reactions
Sphinganine + NADPH → 3-Dehydrosphinganine + NADPdetails
Enzyme Details
2. Serine palmitoyltransferase 1
General function:
Coenzyme transport and metabolism
Specific function:
Serine palmitoyltransferase (SPT). The heterodimer formed with SPTLC2 or SPTLC3 constitutes the catalytic core. The composition of the serine palmitoyltransferase (SPT) complex determines the substrate preference. The SPTLC1-SPTLC2-SPTSSA complex shows a strong preference for C16-CoA substrate, while the SPTLC1-SPTLC3-SPTSSA isozyme uses both C14-CoA and C16-CoA as substrates, with a slight preference for C14-CoA. The SPTLC1-SPTLC2-SPTSSB complex shows a strong preference for C18-CoA substrate, while the SPTLC1-SPTLC3-SPTSSB isozyme displays an ability to use a broader range of acyl-CoAs, without apparent preference (By similarity). Required for adipocyte cell viability and metabolic homeostasis (By similarity).
Gene Name:
SPTLC1
Uniprot ID:
Q3MHG1
Molecular weight:
52788.0
Reactions
Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxidedetails
Enzyme Details
3. 2-amino-3-ketobutyrate coenzyme A ligase, mitochondrial
General function:
Coenzyme transport and metabolism
Specific function:
Not Available
Gene Name:
GCAT
Uniprot ID:
Q0P5L8
Molecular weight:
45166.0
Reactions
Palmityl-CoA + L-Serine → 3-Dehydrosphinganine + Carbon dioxidedetails