Human Metabolome Database Version 3.5

Showing metabocard for LysoSM(d18:0) (HMDB12082)

Record Information
Version 3.5
Creation Date 2009-03-24 10:22:04 -0600
Update Date 2014-02-21 09:51:21 -0700
HMDB ID HMDB12082
Secondary Accession Numbers None
Metabolite Identification
Common Name LysoSM(d18:0)
Description Sphingomyelin (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
Download: MOL | SDF | PDB | SMILES | InChI
Display: 2D Structure | 3D Structure
Synonyms
  1. Lysosphingomyelin
  2. SM(d18:0/0:0)
  3. Sphinganine-1-phosphocholine
  4. Sphingomyelin(d18:0/0:0)
Chemical Formula C23H51N2O5P
Average Molecular Weight 466.6352
Monoisotopic Molecular Weight 466.353559264
IUPAC Name (2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium
Traditional IUPAC Name (2-{[(2S,3R)-2-amino-3-hydroxyoctadecyl phosphonato]oxy}ethyl)trimethylazanium
CAS Registry Number Not 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 Key GSEOJHIBPQRSNH-XZOQPEGZSA-N
Chemical Taxonomy
Kingdom Organic Compounds
Super Class Lipids
Class Sphingolipids
Sub Class Lysosphingomyelins and Lysoglycosphingolipids
Other Descriptors
  • Aliphatic Acyclic Compounds
  • Lysosphingomyelins and lysoglycosphingolipids(Lipidmaps)
Substituents
  • 1,2 Aminoalcohol
  • Choline
  • Organic Hypophosphite
  • Organic Phosphite
  • Phosphocholine
  • Phosphoethanolamine
  • Phosphoric Acid Ester
  • Primary Aliphatic Amine (Alkylamine)
  • Quaternary Ammonium Salt
  • Secondary Alcohol
Direct Parent Lysosphingomyelins and Lysoglycosphingolipids
Ontology
Status Expected and Not Quantified
Origin
  • Endogenous
  • Food
Biofunction
  • Cell signaling
  • Energy source
  • Fuel and energy storage
  • Fuel or energy source
  • Membrane component
  • Membrane integrity/stability
Application
  • Nutrients
  • Stabilizers
  • Surfactants and Emulsifiers
Cellular locations
  • Extracellular
  • Membrane
Physical Properties
State Solid
Experimental Properties
Property Value Reference
Melting Point Not Available Not Available
Boiling Point Not Available Not Available
Water Solubility Not Available Not Available
LogP Not Available Not Available
Predicted Properties
Property Value Source
Water Solubility 7.040E-04 g/L ALOGPS
LogP 1.72 ALOGPS
LogP -0.047 ChemAxon
LogS -5.87 ALOGPS
pKa (strongest acidic) 1.83 ChemAxon
pKa (strongest basic) 9.73 ChemAxon
Hydrogen Acceptor Count 4 ChemAxon
Hydrogen Donor Count 2 ChemAxon
Polar Surface Area 104.84 A2 ChemAxon
Rotatable Bond Count 22 ChemAxon
Refractivity 139.1 ChemAxon
Polarizability 56.39 ChemAxon
Formal Charge 0 ChemAxon
Physiological Charge 1 ChemAxon
Spectra
Not Available
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biofluid Locations Not Available
Tissue Location Not Available
Pathways Not Available
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease References None
Associated OMIM IDs None
DrugBank ID Not Available
DrugBank Metabolite ID Not Available
Phenol Explorer Compound ID Not Available
Phenol Explorer Metabolite ID Not Available
FoodDB ID FDB028751
KNApSAcK ID Not Available
Chemspider ID 21403135 Link_out
KEGG Compound ID Not Available
BioCyc ID Not Available
BiGG ID Not Available
Wikipedia Link Not Available
NuGOwiki Link HMDB12082 Link_out
Metagene Link HMDB12082 Link_out
METLIN ID Not Available
PubChem Compound 44260122 Link_out
PDB ID Not Available
ChEBI ID Not Available
References
Synthesis Reference Not Available
Material Safety Data Sheet (MSDS) Not Available
General References Not Available

Enzymes
Name: Sphingomyelin phosphodiesterase
Reactions: Not Available
Gene Name: SMPD1
Uniprot ID: P17405 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1
Reactions: Not Available
Gene Name: B3GAT1
Uniprot ID: Q9P2W7 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
Reactions: Not Available
Gene Name: ENPP7
Uniprot ID: Q6UWV6 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Sphingomyelin phosphodiesterase 2
Reactions: Not Available
Gene Name: SMPD2
Uniprot ID: O60906 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Proactivator polypeptide
Reactions: Not Available
Gene Name: PSAP
Uniprot ID: P07602 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-3
Reactions: Not Available
Gene Name: PLCD3
Uniprot ID: Q8N3E9 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Sphingomyelin phosphodiesterase 3
Reactions: Not Available
Gene Name: SMPD3
Uniprot ID: Q9NY59 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Sphingomyelin phosphodiesterase 4
Reactions: Not Available
Gene Name: SMPD4
Uniprot ID: Q9NXE4 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Non-lysosomal glucosylceramidase
Reactions: Not Available
Gene Name: GBA2
Uniprot ID: Q9HCG7 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA
Name: Sphingomyelin synthase-related protein 1
Reactions: Not Available
Gene Name: SAMD8
Uniprot ID: Q96LT4 Link_out
Protein Sequence: FASTA
Gene Sequence: FASTA