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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2009-03-24 16:22:12 UTC
Update Date2018-05-20 09:05:36 UTC
HMDB IDHMDB0012090
Secondary Accession Numbers
  • HMDB12090
Metabolite Identification
Common NameSM(d18:0/20:0)
DescriptionSphingomyelin (d18:0/20:0) or SM(d18:0/20:0) 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
N-(Eicosanoyl)-sphinganine-1-phosphocholineHMDB
SphingomyelinHMDB
Sphingomyelin (D18:0/20:0)HMDB
Chemical FormulaC43H89N2O6P
Average Molecular Weight761.1503
Monoisotopic Molecular Weight760.645825102
IUPAC Name(2-{[(2S,3R)-3-hydroxy-2-icosanamidooctadecyl phosphonato]oxy}ethyl)trimethylazanium
Traditional NameC20DH sphingomyelin
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCCCC(=O)N[C@@H](COP([O-])(=O)OCC[N+](C)(C)C)[C@H](O)CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C43H89N2O6P/c1-6-8-10-12-14-16-18-20-21-22-23-25-27-29-31-33-35-37-43(47)44-41(40-51-52(48,49)50-39-38-45(3,4)5)42(46)36-34-32-30-28-26-24-19-17-15-13-11-9-7-2/h41-42,46H,6-40H2,1-5H3,(H-,44,47,48,49)/t41-,42+/m0/s1
InChI KeyUGRZESKDAPEULH-ACEXITHZSA-N
Chemical Taxonomy
DescriptionThis compound belongs to the class of organic compounds 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.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSphingolipids
Sub ClassPhosphosphingolipids
Direct ParentPhosphosphingolipids
Alternative Parents
Substituents
  • Sphingoid-1-phosphate or derivatives
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Fatty amide
  • N-acyl-amine
  • Organic phosphoric acid derivative
  • Phosphoric acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Carboxylic acid derivative
  • Organic zwitterion
  • Alcohol
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Organopnictogen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Amine
  • Organic salt
  • 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 Solubility2.6e-05 g/LALOGPS
logP5.74ALOGPS
logP10.05ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)0.025ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area107.92 ŲChemAxon
Rotatable Bond Count41ChemAxon
Refractivity231.38 m³·mol⁻¹ChemAxon
Polarizability98.38 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectra
Spectra
Spectrum TypeDescriptionSplash Key
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03gu-6030190400-f88a73833d3a8d0b9b90View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03gj-2070191000-40293b760bf93bb7a253View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00m0-6091012000-d3872cc315458c061b36View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0000003900-3a6f795ad70f1c0905d9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0a6r-2043149400-7b799eaf911d98e2ffd9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-03fr-9146020000-d7b54f05b570c698217aView in MoNA
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen Locations
  • Blood
  • Feces
Tissue LocationNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified2.78 +/- 0.03 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not Quantified Newborn (0-30 days old)Not Specified
Premature neonates
details
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDFDB028757
KNApSAcK IDNot Available
Chemspider ID24846879
KEGG Compound IDC00550
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound44260131
PDB IDNot Available
ChEBI ID17636
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. Hannun YA: The sphingomyelin cycle and the second messenger function of ceramide. J Biol Chem. 1994 Feb 4;269(5):3125-8. [PubMed:8106344 ]
  8. Cevc, Gregor (1993). Phospholipids Handbook. Marcel Dekker.
  9. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Only showing the first 10 proteins. There are 50 proteins in total.

Enzymes

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

Only showing the first 10 proteins. There are 50 proteins in total.