You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.

Showing metabocard for LysoSM(d18:1) (HMDB0006482)

Jump To Section:
IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (10) Show 10 proteinsXML
enzymes (10) Show 10 proteins
Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2007-05-23 11:19:36 UTC
Update Date2020-02-26 21:26:25 UTC
HMDB IDHMDB0006482
Secondary Accession Numbers
  • HMDB0012083
  • HMDB06482
  • HMDB12083
Metabolite Identification
Common NameLysoSM(d18:1)
DescriptionLysoSM(d18:1), also known as lysosphingomyelin or SM(D18:1/0:0), belongs to the class of organic compounds known as sphingosylphosphorylcholines. These are sphingolipids containing a sphingosine attached to the phosphate group of a phosphocholine. LysoSM(d18:1) is a very strong basic compound (based on its pKa).
Structure
Data?1582752385
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
Sphing-4-enine-1-phosphocholineChEBI
Sphingosyl-phosphocholineChEBI
SphingosylphosphocholineChEBI
C18-Sphingosine phosphocholineHMDB
D-Erythro-sphingosylphosphorylcholineHMDB
LysosphingomyelinHMDB
SM(D18:1/0:0)HMDB
Sphingenyl-1-phosphorylcholineHMDB
Sphingomyelin(D18:1/0:0)HMDB
Sphingosine phosphorylcholineHMDB
SphingosylphosphorylcholineHMDB
Chemical FormulaC23H50N2O5P
Average Molecular Weight465.6273
Monoisotopic Molecular Weight465.345734232
IUPAC Name{[(2S,3R,4E)-2-amino-3-hydroxyoctadec-4-en-1-yl]oxy}[2-(trimethylazaniumyl)ethoxy]phosphinic acid
Traditional Namelysosphingomyelin
CAS Registry Number1670-26-4
SMILES
CCCCCCCCCCCCC\C=C\[C@@H](O)[C@@H](N)COP(=O)(O)OCC[N+](C)(C)C
InChI Identifier
InChI=1S/C23H49N2O5P/c1-5-6-7-8-9-10-11-12-13-14-15-16-17-18-23(26)22(24)21-30-31(27,28)29-20-19-25(2,3)4/h17-18,22-23,26H,5-16,19-21,24H2,1-4H3/p+1/b18-17+/t22-,23+/m0/s1
InChI KeyJLVSPVFPBBFMBE-HXSWCURESA-O
Chemical Taxonomy
Description belongs to the class of organic compounds known as sphingosylphosphorylcholines. These are sphingolipids containing a sphingosine attached to the phosphate group of a phosphocholine.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassPhosphosphingolipids
Direct ParentSphingosylphosphorylcholines
Alternative Parents
Substituents
  • Sphingosylphosphorylcholine
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary alcohol
  • Alcohol
  • Amine
  • Organic salt
  • Hydrocarbon derivative
  • Primary amine
  • Organic oxide
  • Organopnictogen compound
  • Organic oxygen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic nitrogen compound
  • Primary aliphatic amine
  • Organic cation
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect

Organoleptic effect:

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 Solubility0.00084 g/LALOGPS
logP1.3ALOGPS
logP-0.24ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)1.83ChemAxon
pKa (Strongest Basic)9.68ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area102.01 ŲChemAxon
Rotatable Bond Count21ChemAxon
Refractivity141.18 m³·mol⁻¹ChemAxon
Polarizability55.37 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-00ej-9782140000-24f3d9fcbb4a3475e571Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB023932
KNApSAcK IDNot Available
Chemspider ID4444221
KEGG Compound IDC03640
BioCyc IDNot Available
BiGG ID2704995
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5280613
PDB IDSPU
ChEBI ID52897
Food Biomarker OntologyNot Available
VMH IDSPC_HS
References
Synthesis ReferenceSphingomyelin, intermediates thereof and methods for preparation of same. Rochlin, Elimelech; Hildesheim, Jean; Berlin, Alisa. (Biolab Ltd., Israel). PCT Int. Appl. (2005), 39 pp.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Morita SY, Soda K, Teraoka R, Kitagawa S, Terada T: Specific and sensitive enzymatic measurement of sphingomyelin in cultured cells. Chem Phys Lipids. 2012 Jul;165(5):571-6. doi: 10.1016/j.chemphyslip.2012.06.003. Epub 2012 Jun 19. [PubMed:22727956 ]

Enzymes

Enzyme Details
1. Sphingomyelin phosphodiesterase
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53
Enzyme Details
2. Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
General function:
Involved in galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity
Specific function:
Involved in the biosynthesis of L2/HNK-1 carbohydrate epitope on glycoproteins. Can also play a role in glycosaminoglycan biosynthesis. Substrates include asialo-orosomucoid (ASOR), asialo-fetuin, and asialo-neural cell adhesion molecule. Requires sphingomyelin for activity: stearoyl-sphingomyelin was the most effective, followed by palmitoyl-sphingomyelin and lignoceroyl-sphingomyelin. Activity was demonstrated only for sphingomyelin with a saturated fatty acid and not for that with an unsaturated fatty acid, regardless of the length of the acyl group (By similarity).
Gene Name:
B3GAT1
Uniprot ID:
Q9P2W7
Molecular weight:
38255.675
Enzyme Details
3. Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
General function:
Involved in catalytic activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activity toward palmitoyl lyso-phosphocholine. Does not appear to have nucleotide pyrophosphatase activity.
Gene Name:
ENPP7
Uniprot ID:
Q6UWV6
Molecular weight:
51493.415
Enzyme Details
4. Sphingomyelin phosphodiesterase 2
General function:
Involved in metal ion binding
Specific function:
Converts sphingomyelin to ceramide. Hydrolyze 1-acyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PC) and 1-O-alkyl-2-lyso-sn-glycero-3-phosphocholine (lyso-platelet-activating factor). The physiological substrate seems to be Lyso-PAF.
Gene Name:
SMPD2
Uniprot ID:
O60906
Molecular weight:
47645.29
Enzyme Details
5. Proactivator polypeptide
General function:
Involved in lipid metabolic process
Specific function:
Saposin-D is a specific sphingomyelin phosphodiesterase activator (EC 3.1.4.12)
Gene Name:
PSAP
Uniprot ID:
P07602
Molecular weight:
58112.1
Enzyme Details
6. 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3
General function:
Involved in calcium ion binding
Specific function:
Hydrolyzes the phosphatidylinositol 4,5-bisphosphate (PIP2) to generate 2 second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3). DAG mediates the activation of protein kinase C (PKC), while IP3 releases Ca(2+) from intracellular stores. Essential for trophoblast and placental development. May participate in cytokinesis by hydrolyzing PIP2 at the cleavage furrow.
Gene Name:
PLCD3
Uniprot ID:
Q8N3E9
Molecular weight:
89257.54
Enzyme Details
7. Sphingomyelin phosphodiesterase 3
General function:
Involved in metal ion binding
Specific function:
Catalyzes the hydrolysis of sphingomyelin to form ceramide and phosphocholine. Ceramide mediates numerous cellular functions, such as apoptosis and growth arrest, and is capable of regulating these 2 cellular events independently. Also hydrolyzes sphingosylphosphocholine. Regulates the cell cycle by acting as a growth suppressor in confluent cells. Probably acts as a regulator of postnatal development and participates in bone and dentin mineralization.
Gene Name:
SMPD3
Uniprot ID:
Q9NY59
Molecular weight:
71080.1
Enzyme Details
8. Sphingomyelin phosphodiesterase 4
General function:
Involved in metal ion binding
Specific function:
Catalyzes the hydrolysis of membrane sphingomyelin to form phosphorylcholine and ceramide.
Gene Name:
SMPD4
Uniprot ID:
Q9NXE4
Molecular weight:
86192.575
Enzyme Details
9. Non-lysosomal glucosylceramidase
General function:
Involved in catalytic activity
Specific function:
Non-lysosomal glucosylceramidase that catalyzes the conversion of glucosylceramide to free glucose and ceramide. Involved in sphingomyelin generation and prevention of glycolipid accumulation. May also catalyze the hydrolysis of bile acid 3-O-glucosides, however, the relevance of such activity is unclear in vivo.
Gene Name:
GBA2
Uniprot ID:
Q9HCG7
Molecular weight:
104648.13
Enzyme Details
10. Sphingomyelin synthase-related protein 1
General function:
Involved in sphingomyelin biosynthetic process
Specific function:
Not Available
Gene Name:
SAMD8
Uniprot ID:
Q96LT4
Molecular weight:
48320.2