Hmdb loader
Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 00:14:26 UTC
Update Date2022-11-30 20:06:55 UTC
HMDB IDHMDB0289908
Secondary Accession NumbersNone
Metabolite Identification
Common NameCer(d17:1/TXB2)
DescriptionCer(d17:1/TXB2) is an oxidized ceramide (Cer). As all ceramides, oxidized ceramides 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). In humans, ceramides are phosphorylated to ceramide phosphates (CerPs) through the action of a specific ceramide kinase (CerK). Ceramide phosphates are important metabolites of ceramides as they act as a mediators of the inflammatory response. Ceramides are also one of the hydrolysis byproducts of sphingomyelins (SMs) through the action of the enzyme sphingomyelin phosphodiesterase, which has been identified in the subcellular fractions of human epidermis (PMID: 25935) and many other tissues. Ceramides can also be synthesized from serine and palmitate in a de novo pathway and are regarded as important cellular signals for inducing apoptosis (PMID: 14998372). Ceramides are key in the biosynthesis of glycosphingolipids and gangliosides. In terms of its appearance and structure, Cer(d18:1/22:1(13Z)) is a colorless solid that consists of an unsaturated 18-carbon sphingoid base with an attached unsaturated 13Z-docosenoyl fatty acid side chain. In most mammalian SPs, the 18-carbon sphingoid bases are predominant (PMID: 9759481).
Structure
Thumb
Synonyms
ValueSource
(5Z)-7-[(2R,3S,4S)-4,6-Dihydroxy-2-[(3S)-3-hydroxyoct-1-en-1-yl]oxan-3-yl]-N-[(2S,3R)-1,3-dihydroxyheptadec-4-en-2-yl]hept-5-enimidateGenerator
Chemical FormulaC37H67NO7
Average Molecular Weight637.943
Monoisotopic Molecular Weight637.491753501
IUPAC Name(5Z)-7-[(2R,3S,4S)-4,6-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]oxan-3-yl]-N-[(2S,3R,4E)-1,3-dihydroxyheptadec-4-en-2-yl]hept-5-enamide
Traditional Name(5Z)-7-[(2R,3S,4S)-4,6-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]oxan-3-yl]-N-[(2S,3R,4E)-1,3-dihydroxyheptadec-4-en-2-yl]hept-5-enamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCC\C=C\[C@@H](O)[C@H](CO)NC(=O)CCC\C=C/C[C@H]1[C@@H](O)CC(O)O[C@@H]1\C=C\[C@@H](O)CCCCC
InChI Identifier
InChI=1S/C37H67NO7/c1-3-5-7-8-9-10-11-12-13-14-15-20-24-33(41)32(29-39)38-36(43)25-21-17-16-19-23-31-34(42)28-37(44)45-35(31)27-26-30(40)22-18-6-4-2/h16,19-20,24,26-27,30-35,37,39-42,44H,3-15,17-18,21-23,25,28-29H2,1-2H3,(H,38,43)/b19-16-,24-20+,27-26+/t30-,31-,32-,33+,34-,35+,37?/m0/s1
InChI KeyZDNVDYSPORTCCW-ICLITUENSA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effect
Disposition
Process
RoleNot Available
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
logP5.99ALOGPS
logP7.09ChemAxon
logS-5.5ALOGPS
pKa (Strongest Acidic)12.33ChemAxon
pKa (Strongest Basic)-1.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area139.48 ŲChemAxon
Rotatable Bond Count27ChemAxon
Refractivity185.28 m³·mol⁻¹ChemAxon
Polarizability78.91 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]+263.59932859911
AllCCS[M+H-H2O]+263.16332859911
AllCCS[M+Na]+264.06432859911
AllCCS[M+NH4]+263.96632859911
AllCCS[M-H]-251.20632859911
AllCCS[M+Na-2H]-256.12332859911
AllCCS[M+HCOO]-261.62932859911
DeepCCS[M+H]+254.74330932474
DeepCCS[M-H]-252.91830932474
DeepCCS[M-2H]-286.15830932474
DeepCCS[M+Na]+260.34930932474

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. Predicted by Afia on May 17, 2022.7.1 minutes32390414
Predicted by Siyang on May 30, 202220.3501 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.34 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4364.6 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid169.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid278.8 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid193.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid624.4 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid953.2 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 Acid695.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)457.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid2172.3 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid857.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2133.6 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid639.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid573.7 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate206.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA180.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.4 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 10V, Positive-QTOFsplash10-000i-0000009000-41e364e4063d55bdae052021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 20V, Positive-QTOFsplash10-0f79-0050009000-0b5fe51e80ba09f131ef2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 40V, Positive-QTOFsplash10-0v4i-0090005000-3311c2ed4a28924922972021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 10V, Positive-QTOFsplash10-0006-0000009000-69c8af784ec5183efb872021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 20V, Positive-QTOFsplash10-0006-0000009000-69c8af784ec5183efb872021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 40V, Positive-QTOFsplash10-004i-0000019000-49a93ef10401b0df4f592021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 10V, Negative-QTOFsplash10-000i-0000009000-26c5d87583448661ffba2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 20V, Negative-QTOFsplash10-000i-0010009000-043d809256b212f757522021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cer(d17:1/TXB2) 40V, Negative-QTOFsplash10-0udr-0022009000-54b3f7a95297b37fc8d32021-10-21Wishart LabView Spectrum
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