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Record Information
Version4.0
StatusExpected but not Quantified
Creation Date2009-03-24 16:22:04 UTC
Update Date2017-12-07 02:35:41 UTC
HMDB IDHMDB0012082
Secondary Accession Numbers
  • HMDB12082
Metabolite Identification
Common NameLysoSM(d18:0)
DescriptionSphingomyelin (d18:0/0:0) or LysoSM(d18:0) is a type of sphingolipid found in animal cell membranes, especially in the membranous myelin sheath which surrounds some nerve cell axons. It usually consists of phosphorylcholine and ceramide. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SPH has a ceramide core (sphingosine bonded to a fatty acid via an amide linkage). In addition it contains one polar head group, which is either phosphocholine or phosphoethanolamine. The plasma membrane of cells is highly enriched in sphingomyelin and is considered largely to be found in the exoplasmic leaflet of the cell membrane. However, there is some evidence that there may also be a sphingomyelin pool in the inner leaflet of the membrane. Moreover, neutral sphingomyelinase-2 - an enzyme that breaks down sphingomyelin into ceramide has been found to localise exclusively to the inner leaflet further suggesting that there may be sphingomyelin present there. Sphingomyelin can accumulate in a rare hereditary disease called Niemann-Pick Disease, types A and B. Niemann-Pick disease is a genetically-inherited disease caused by a deficiency in the enzyme Sphingomyelinase, which causes the accumulation of Sphingomyelin in spleen, liver, lungs, bone marrow, and the brain, causing irreversible neurological damage. SMs play a role in signal transduction. Sphingomyelins are synthesized by the transfer of phosphorylcholine from phosphatidylcholine to a ceramide in a reaction catalyzed by sphingomyelin synthase.
Structure
Thumb
Synonyms
ValueSource
LysosphingomyelinHMDB
SM(D18:0/0:0)HMDB
Sphinganine-1-phosphocholineHMDB
Sphingomyelin(D18:0/0:0)HMDB
Chemical FormulaC23H51N2O5P
Average Molecular Weight466.6352
Monoisotopic Molecular Weight466.353559264
IUPAC Name(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCC[C@@H](O)[C@@H](N)COP([O-])(=O)OCC[N+](C)(C)C
InChI Identifier
InChI=1S/C23H51N2O5P/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/h22-23,26H,5-21,24H2,1-4H3/t22-,23+/m0/s1
InChI KeyGSEOJHIBPQRSNH-XZOQPEGZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities known as phosphosphingolipids. These are sphingolipids with a structure based on a sphingoid base that is attached to a phosphate head group. They differ from phosphonospingolipids which have a phosphonate head group.
KingdomChemical entities
Super ClassOrganic compounds
ClassLipids and lipid-like molecules
Sub ClassSphingolipids
Direct ParentPhosphosphingolipids
Alternative Parents
Substituents
  • Sphingoid-1-phosphate or derivatives
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • 1,2-aminoalcohol
  • Secondary alcohol
  • Organic nitrogen compound
  • Organic zwitterion
  • Organic salt
  • Primary amine
  • Hydrocarbon derivative
  • Organic oxide
  • Organopnictogen compound
  • Organooxygen compound
  • Organonitrogen compound
  • Organic oxygen compound
  • Primary aliphatic amine
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Disposition

Biological Location:

  Subcellular:

  Cell and elements:

Source:

  Biological:

    Animal:

Route of exposure:

  Enteral:

Role

Biological role:

Industrial application:

  Food and nutrition:

Process

Naturally occurring process:

  Biological process:

    Cellular process:

    Biochemical pathway:

    Chemical reaction:

    Biochemical process:

Physiological effect

Organoleptic effect:

  Touch:

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 Solubility0.0007 g/LALOGPS
logP1.72ALOGPS
logP-0.047ChemAxon
logS-5.9ALOGPS
pKa (Strongest Acidic)1.83ChemAxon
pKa (Strongest Basic)9.73ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area104.84 ŲChemAxon
Rotatable Bond Count22ChemAxon
Refractivity139.1 m³·mol⁻¹ChemAxon
Polarizability56.39 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (1 TMS) - 70eV, Positivesplash10-006t-7491010000-bc23518378651a125026View in MoNA
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biofluid LocationsNot Available
Tissue LocationNot Available
PathwaysNot Available
NameSMPDB/PathwhizKEGG
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB028751
KNApSAcK IDNot Available
Chemspider ID21403135
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44260122
PDB IDNot Available
ChEBI ID132478
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Divecha N, Irvine RF: Phospholipid signaling. Cell. 1995 Jan 27;80(2):269-78. [PubMed:7834746 ]
  6. Ghosh S, Strum JC, Bell RM: Lipid biochemistry: functions of glycerolipids and sphingolipids in cellular signaling. FASEB J. 1997 Jan;11(1):45-50. [PubMed:9034165 ]
  7. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  8. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

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
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
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
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
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
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
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
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
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
General function:
Involved in sphingomyelin biosynthetic process
Specific function:
Not Available
Gene Name:
SAMD8
Uniprot ID:
Q96LT4
Molecular weight:
48320.2