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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 02:51:09 UTC
Update Date2022-11-30 20:07:06 UTC
HMDB IDHMDB0290300
Secondary Accession NumbersNone
Metabolite Identification
Common NameSM(d16:2(4E,8Z)/20:4(5Z,8Z,11Z,14Z)-OH(19S))
DescriptionSM(d16:2(4E,8Z)/20:4(5Z,8Z,11Z,14Z)-OH(19S)) is a type of oxidized sphingolipid found in animal cell membranes. It usually consists of phosphorylcholine and ceramide. SM(d16:2(4E,8Z)/20:4(5Z,8Z,11Z,14Z)-OH(19S)) consists of a sphingosine backbone and a 19-Hydroxyeicosatetraenoyl 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 FormulaC41H73N2O7P
Average Molecular Weight737.016
Monoisotopic Molecular Weight736.515539697
IUPAC Name(2-{[(2S,3R,4E,8Z)-3-hydroxy-2-[(5Z,8Z,11Z,14Z,19S)-19-hydroxyicosa-5,8,11,14-tetraenamido]hexadeca-4,8-dien-1-yl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[(2S,3R,4E,8Z)-3-hydroxy-2-[(5Z,8Z,11Z,14Z,19S)-19-hydroxyicosa-5,8,11,14-tetraenamido]hexadeca-4,8-dien-1-yl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
[H][C@@](COP([O-])(=O)OCC[N+](C)(C)C)(NC(=O)CCC\C=C/C\C=C/C\C=C/C\C=C/CCC[C@H](C)O)[C@H](O)\C=C\CC\C=C/CCCCCCC
InChI Identifier
InChI=1S/C41H73N2O7P/c1-6-7-8-9-10-11-17-21-24-27-30-33-40(45)39(37-50-51(47,48)49-36-35-43(3,4)5)42-41(46)34-31-28-25-22-19-16-14-12-13-15-18-20-23-26-29-32-38(2)44/h13-17,20-23,25,30,33,38-40,44-45H,6-12,18-19,24,26-29,31-32,34-37H2,1-5H3,(H-,42,46,47,48)/b15-13-,16-14-,21-17-,23-20-,25-22-,33-30+/t38-,39-,40+/m0/s1
InChI KeyQPQROFKUZBOHHQ-LUQBEQDFSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phosphocholines. Phosphocholines are compounds containing a [2-(trimethylazaniumyl)ethoxy]phosphonic acid or derivative.
KingdomOrganic compounds
Super ClassOrganic nitrogen compounds
ClassOrganonitrogen compounds
Sub ClassQuaternary ammonium salts
Direct ParentPhosphocholines
Alternative Parents
Substituents
  • Phosphocholine
  • Phosphoethanolamine
  • Dialkyl phosphate
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • N-acyl-amine
  • Fatty amide
  • Tetraalkylammonium salt
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Carboxamide group
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organic salt
  • Organic zwitterion
  • Organooxygen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
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
logP4.48ALOGPS
logP4.59ChemAxon
logS-7.1ALOGPS
pKa (Strongest Acidic)1.87ChemAxon
pKa (Strongest Basic)-0.94ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area128.15 ŲChemAxon
Rotatable Bond Count33ChemAxon
Refractivity230.47 m³·mol⁻¹ChemAxon
Polarizability87.02 ųChemAxon
Number of Rings0ChemAxon
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]+281.52832859911
AllCCS[M+H-H2O]+281.18432859911
AllCCS[M+Na]+281.89432859911
AllCCS[M+NH4]+281.81732859911
AllCCS[M-H]-264.44632859911
AllCCS[M+Na-2H]-269.61732859911
AllCCS[M+HCOO]-275.31332859911
DeepCCS[M+H]+272.41730932474
DeepCCS[M-H]-270.16530932474
DeepCCS[M-2H]-303.40530932474
DeepCCS[M+Na]+278.3330932474

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. 5.13 minutes32390414
Predicted by Siyang on May 30, 202226.2227 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.8 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4660.3 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid181.8 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid308.3 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid213.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid568.1 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1337.1 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 Acid770.3 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)538.1 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid3050.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid1005.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2648.8 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid785.2 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid685.6 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate344.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA110.9 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water11.4 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 Compound156997945
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