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Record Information
Version4.0
StatusDetected but not Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2019-07-23 05:45:01 UTC
HMDB IDHMDB0001480
Secondary Accession Numbers
  • HMDB01480
Metabolite Identification
Common Name3-Dehydrosphinganine
Description3-Dehydrosphinganine is an intermediate in the metabolism of Glycosphingolipids. It is a substrate for Serine palmitoyltransferase 1 and Serine palmitoyltransferase 2.
Structure
Data?1563860701
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
Disposition

Route of exposure:

Source:

Biological location:

Process

Naturally occurring process:

Role

Industrial application:

Biological role:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
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
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-01p9-9120000000-135052b999433b5dd30bJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-03di-9321000000-e0d96cb3bea3c320412aJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0f89-2096000000-8323a157b44b31f2331aJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01qa-4491000000-39be7a6025f78d062cb5JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-01ox-9510000000-a675e52903f069501f67JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-1090000000-e36f44a44812cc09023cJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-015j-4090000000-4a24200105a7fd0afd1eJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-052f-9020000000-edd2ec1e7a7fae113d2fJSpectraViewer | MoNA
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
  • Membrane (predicted from logP)
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
FecesDetected but not Quantified Adult (>18 years old)Both
Normal
details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB 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 References
  1. Stoffel W, Assmann G, Binczek E: Metabolism of sphingosine bases. 13. Enzymatic synthesis of 1-phosphate esters of 4t-sphingenine (sphingosine), sphinganine (dihydrosphingosine), 4-hydroxysphinganine (phytosphingosine) and 3-dehydrosphinganine by erythrocytes. Hoppe Seylers Z Physiol Chem. 1970 May;351(5):635-42. [PubMed:4315749 ]
  2. Newman H: A short, simple synthetic route to 3-dehydrosphinganine and related compounds. Chem Phys Lipids. 1974 Feb;12(1):48-52. [PubMed:4362562 ]

Only showing the first 10 proteins. There are 45 proteins in total.

Enzymes

General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in transferase activity, transferring nitrogenous groups
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.
Gene Name:
SPTLC1
Uniprot ID:
O15269
Molecular weight:
52743.41
Reactions
hexadecanoyl-CoA + L-Serine → Coenzyme A + 3-Dehydrosphinganine + CO(2)details
hexadecanoyl-CoA + L-Serine → 3-Dehydrosphinganine + Coenzyme A + Carbon dioxidedetails
General function:
Involved in transferase activity
Specific function:
Serine palmitoyltransferase (SPT). The heterodimer formed with LCB1/SPTLC1 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-SPTLC2-SPTSSB complex displays a preference for C18-CoA substrate.
Gene Name:
SPTLC2
Uniprot ID:
O15270
Molecular weight:
62923.765
Reactions
hexadecanoyl-CoA + L-Serine → Coenzyme A + 3-Dehydrosphinganine + CO(2)details
hexadecanoyl-CoA + L-Serine → 3-Dehydrosphinganine + Coenzyme A + Carbon dioxidedetails
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGP
Uniprot ID:
P57054
Molecular weight:
18089.055
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGC
Uniprot ID:
Q92535
Molecular weight:
33582.18
General function:
Involved in sphingolipid activator protein activity
Specific function:
Binds gangliosides and stimulates ganglioside GM2 degradation. It stimulates only the breakdown of ganglioside GM2 and glycolipid GA2 by beta-hexosaminidase A. It extracts single GM2 molecules from membranes and presents them in soluble form to beta-hexosaminidase A for cleavage of N-acetyl-D-galactosamine and conversion to GM3
Gene Name:
GM2A
Uniprot ID:
P17900
Molecular weight:
20838.1

Only showing the first 10 proteins. There are 45 proteins in total.