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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 06:07:52 UTC
Update Date2022-11-30 20:07:17 UTC
HMDB IDHMDB0290740
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d20:1/18:1(12Z)-O(9S,10R))
DescriptionSM(d20:1/18:1(12Z)-O(9S,10R)) is a type of oxidized sphingolipid found in animal cell membranes. It usually consists of phosphorylcholine and ceramide. SM(d20:1/18:1(12Z)-O(9S,10R)) consists of a sphingosine backbone and a 9,10-epoxy-octadecenoyl chain. In humans, sphingomyelin is the only membrane phospholipid not derived from glycerol. Like all sphingolipids, SM 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 localize 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
SynonymsNot Available
Chemical FormulaC43H83N2O7P
Average Molecular Weight771.118
Monoisotopic Molecular Weight770.593790019
IUPAC Name(2-{[(2S,3R,4E)-3-hydroxy-2-(8-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}octanamido)icos-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E)-3-hydroxy-2-(8-{3-[(2Z)-oct-2-en-1-yl]oxiran-2-yl}octanamido)icos-4-en-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCCCCCCC1OC1C\C=C/CCCCC)[C@H](O)\C=C\CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C43H83N2O7P/c1-6-8-10-12-14-15-16-17-18-19-20-21-22-24-28-32-40(46)39(38-51-53(48,49)50-37-36-45(3,4)5)44-43(47)35-31-27-23-26-30-34-42-41(52-42)33-29-25-13-11-9-7-2/h25,28-29,32,39-42,46H,6-24,26-27,30-31,33-38H2,1-5H3,(H-,44,47,48,49)/b29-25-,32-28+/t39-,40+,41?,42?/m0/s1
InChI KeyRFLWMXKCTWZLIW-OKWDTRNFSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP5.21ALOGPS
logP7.09ChemAxon
logS-7.4ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area120.45 ŲChemAxon
Rotatable Bond Count38ChemAxon
Refractivity232.98 m³·mol⁻¹ChemAxon
Polarizability95.99 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+291.96632859911
AllCCS[M+H-H2O]+291.88832859911
AllCCS[M+Na]+292.01532859911
AllCCS[M+NH4]+292.00832859911
AllCCS[M-H]-281.69332859911
AllCCS[M+Na-2H]-286.05732859911
AllCCS[M+HCOO]-290.87532859911
DeepCCS[M+H]+287.20630932474
DeepCCS[M-H]-284.91330932474
DeepCCS[M-2H]-318.15330932474
DeepCCS[M+Na]+293.11930932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. 8.85 minutes32390414
Predicted by Siyang on May 30, 202231.3092 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.68 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid5053.4 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid245.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid361.0 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid195.9 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1033.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1640.0 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid1097.8 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)603.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3561.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1033.4 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid3164.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid1001.5 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid733.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate198.0 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA229.0 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water10.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular LocationsNot Available
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 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
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available