Showing metabocard for SM(d20:0/24:1(15Z)) (BMDB0063570)

IdentificationTaxonomyPhysical propertiesSpectraConcentrationsLinksReferencesXML
Record Information
Version1.0
Creation Date2018-09-13 16:17:02 UTC
Update Date2020-06-04 19:15:11 UTC
MCDB ID BMDB0063570
Secondary Accession Numbers
  • BMDB63570
Metabolite Identification
Common NameSM(d20:0/24:1(15Z))
DescriptionSM(d20:0/24:1(15Z)) is a sphingomyelin (SM). Sphingomyelins are members of the class of compounds known as sphingolipids (SPs), or glycosylceramides. SPs are lipids containing a backbone of sphingoid bases (e.g. sphingosine or sphinganine) that are often covalently bound to a fatty acid derivative through N-acylation. SPs are found in cell membranes, particularly in peripheral nerve cells and the cells found in the central nervous system (including the brain and spinal cord). Sphingolipids are extremely versatile molecules that have functions controlling fundamental cellular processes such as cell division, differentiation, and cell death. Impairments associated with sphingolipid metabolism are associated with many common human diseases such as diabetes, various cancers, microbial infections, diseases of the cardiovascular and respiratory systems, Alzheimer’s disease and other neurological syndromes. The biosynthesis and catabolism of sphingolipids involves a large number of intermediate metabolites where many different enzymes are involved. Simple sphingolipids, which include the sphingoid bases and ceramides, make up the early products of the sphingolipid synthetic pathways, while complex sphingolipids may be formed by the addition of head groups to the ceramide template (Wikipedia). SM is the major sphingolipid in mammals it is found in animal cell membranes, especially in the membranous myelin sheath that surrounds some nerve cell axons. It usually consists of phosphocholine and ceramide, or a phosphoethanolamine head group. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. SM 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. In terms of its appearance and structure, SM(d20:0/24:1(15Z)) consists of a saturated 20-carbon sphingoid base with an attached unsaturated 15Z-tetracosenoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481 ).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
ValueSource
SphingomyelinMetBuilder
N-(15Z-Tetracosenoyl)-1-phosphocholine-eicosasphinganineMetBuilder
Sphingomyelin(D20:0/24:1(15Z))MetBuilder
N-(15Z-Tetracosenoyl)-1-phosphocholine-eicosadihydrosphingosineMetBuilder
N-(15Z-Tetracosenoyl)-1-phosphocholine-eicosad-erythro-sphinganineMetBuilder
Chemical FormulaC49H99N2O6P
Average Molecular Weight843.313
Monoisotopic Molecular Weight842.724075914
IUPAC Name(2-{[(2S)-3-hydroxy-2-[(15Z)-tetracos-15-enamido]icosyl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S)-3-hydroxy-2-[(15Z)-tetracos-15-enamido]icosyl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCC(O)[C@H](COP([O-])(=O)OCC[N+](C)(C)C)NC(=O)CCCCCCCCCCCCC\C=C/CCCCCCCC
InChI Identifier
InChI=1S/C49H99N2O6P/c1-6-8-10-12-14-16-18-20-22-23-24-25-26-27-29-31-33-35-37-39-41-43-49(53)50-47(46-57-58(54,55)56-45-44-51(3,4)5)48(52)42-40-38-36-34-32-30-28-21-19-17-15-13-11-9-7-2/h20,22,47-48,52H,6-19,21,23-46H2,1-5H3,(H-,50,53,54,55)/b22-20-/t47-,48?/m0/s1
InChI KeyJWKOQODXKXAOQW-KBYGLLGRSA-N
Chemical Taxonomy
Description 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
  • Dialkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Secondary alcohol
  • Organic 1,3-dipolar compound
  • Propargyl-type 1,3-dipolar organic compound
  • Carboximidic acid derivative
  • Carboximidic acid
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP6.46ALOGPS
logP11.27ChemAxon
logS-7.5ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area107.92 ŲChemAxon
Rotatable Bond Count46ChemAxon
Refractivity260.11 m³·mol⁻¹ChemAxon
Polarizability109.21 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyDeposition DateView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01rf-6003109040-4be5fd82b0d2bd3da3f42019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03dl-2016109100-6bc297f1949e92bad3a72019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-03ki-7019002300-9301f8c4b41d67f428e52019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0006-0000000490-adaf946b699306fcbecf2019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06rm-2014103920-eb90c698244c7430bd642019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-01tc-9128102000-a3b8d8a38d3f8c04fba12019-02-23View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000x-0600000090-2704071632980e25d69d2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000x-0600000090-2704071632980e25d69d2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-0900000030-efc301365f52354a54f82021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0002-0000001190-8190dd68358d7acd78032021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-014k-0000009290-91af3357fe984723e3722021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-014i-0000009110-12505230bf25698e6bc92021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-014i-0000001090-d1f09da0e63133eac2f02021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0160-0000007090-0f2db5ad91a5f55f460f2021-10-21View Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-001i-0000009020-98aa52933dfec4cdb3572021-10-21View Spectrum
Concentrations
StatusValueReferenceDetails
Detected and Quantified0.074 +/- 0.003 uM details
Detected and Quantified0.057 +/- 0.003 uM details
Detected and Quantified0.085 +/- 0.003 uM details
Detected and Quantified0.065 +/- 0.003 uM details
HMDB IDHMDB0304645
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FoodDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Dickson RC: Sphingolipid functions in Saccharomyces cerevisiae: comparison to mammals. Annu Rev Biochem. 1998;67:27-48. doi: 10.1146/annurev.biochem.67.1.27. [PubMed:9759481 ]