Hmdb loader
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2008-08-06 10:44:15 UTC
Update Date2021-09-14 14:59:29 UTC
HMDB IDHMDB0006752
Secondary Accession Numbers
  • HMDB0004608
  • HMDB04608
  • HMDB06752
Metabolite Identification
Common NameDihydroceramide
DescriptionDihydroceramide, also known as N-acylsphinganine, belongs to the class of organic compounds known as secondary carboxylic acid amides. Secondary carboxylic acid amides are compounds containing a secondary carboxylic acid amide functional group, with the general structure RC(=O)N(R')H (R,R'=alkyl, aryl). Dihydroceramide is an extremely weak basic (essentially neutral) compound (based on its pKa). Dihydroceramide exists in all eukaryotes, ranging from yeast to humans.
Structure
Data?1582752403
Synonyms
ValueSource
N-AcylsphinganineHMDB
N-[(2S,3R)-1,3-Dihydroxyoctadecan-2-yl]formamideHMDB
Chemical FormulaC19H39NO3
Average Molecular Weight329.5179
Monoisotopic Molecular Weight329.292994119
IUPAC NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]formamide
Traditional NameN-[(2S,3R)-1,3-dihydroxyoctadecan-2-yl]formamide
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)NC=O
InChI Identifier
InChI=1S/C19H39NO3/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-19(23)18(16-21)20-17-22/h17-19,21,23H,2-16H2,1H3,(H,20,22)/t18-,19+/m0/s1
InChI KeyXSDVOEIEBUGRQX-RBUKOAKNSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as secondary carboxylic acid amides. Secondary carboxylic acid amides are compounds containing a secondary carboxylic acid amide functional group, with the general structure RC(=O)N(R')H (R,R'=alkyl, aryl).
KingdomOrganic compounds
Super ClassOrganic acids and derivatives
ClassCarboxylic acids and derivatives
Sub ClassCarboxylic acid derivatives
Direct ParentSecondary carboxylic acid amides
Alternative Parents
Substituents
  • Secondary carboxylic acid amide
  • Secondary alcohol
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Organonitrogen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect

Adverse health effect

Disposition

Biological location

Source

Route of exposure

Process

Naturally occurring process

Physical Properties
StateSolid
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
Water Solubility0.0046 g/LALOGPS
logP10(4.68) g/LALOGPS
logP10(4.54) g/LChemAxon
logS10(-4.8) g/LALOGPS
pKa (Strongest Acidic)14.11ChemAxon
pKa (Strongest Basic)-0.41ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area69.56 ŲChemAxon
Rotatable Bond Count17ChemAxon
Refractivity95.88 m³·mol⁻¹ChemAxon
Polarizability42.49 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+187.73331661259
DarkChem[M-H]-186.86431661259

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
DihydroceramideCCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)NC=O3014.3Standard polar33892256
DihydroceramideCCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)NC=O2493.1Standard non polar33892256
DihydroceramideCCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)NC=O2769.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Dihydroceramide,1TMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO)NC=O2623.3Semi standard non polar33892256
Dihydroceramide,1TMS,isomer #2CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO[Si](C)(C)C)NC=O2618.9Semi standard non polar33892256
Dihydroceramide,1TMS,isomer #3CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)N(C=O)[Si](C)(C)C2621.5Semi standard non polar33892256
Dihydroceramide,2TMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)NC=O2664.6Semi standard non polar33892256
Dihydroceramide,2TMS,isomer #2CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO)N(C=O)[Si](C)(C)C2691.8Semi standard non polar33892256
Dihydroceramide,2TMS,isomer #3CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO[Si](C)(C)C)N(C=O)[Si](C)(C)C2695.0Semi standard non polar33892256
Dihydroceramide,3TMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C=O)[Si](C)(C)C2779.6Semi standard non polar33892256
Dihydroceramide,3TMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C=O)[Si](C)(C)C2729.1Standard non polar33892256
Dihydroceramide,3TMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C)[C@H](CO[Si](C)(C)C)N(C=O)[Si](C)(C)C2772.2Standard polar33892256
Dihydroceramide,1TBDMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)NC=O2867.8Semi standard non polar33892256
Dihydroceramide,1TBDMS,isomer #2CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO[Si](C)(C)C(C)(C)C)NC=O2845.8Semi standard non polar33892256
Dihydroceramide,1TBDMS,isomer #3CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO)N(C=O)[Si](C)(C)C(C)(C)C2864.4Semi standard non polar33892256
Dihydroceramide,2TBDMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO[Si](C)(C)C(C)(C)C)NC=O3154.6Semi standard non polar33892256
Dihydroceramide,2TBDMS,isomer #2CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO)N(C=O)[Si](C)(C)C(C)(C)C3153.6Semi standard non polar33892256
Dihydroceramide,2TBDMS,isomer #3CCCCCCCCCCCCCCC[C@@H](O)[C@H](CO[Si](C)(C)C(C)(C)C)N(C=O)[Si](C)(C)C(C)(C)C3138.5Semi standard non polar33892256
Dihydroceramide,3TBDMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO[Si](C)(C)C(C)(C)C)N(C=O)[Si](C)(C)C(C)(C)C3444.9Semi standard non polar33892256
Dihydroceramide,3TBDMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO[Si](C)(C)C(C)(C)C)N(C=O)[Si](C)(C)C(C)(C)C3225.9Standard non polar33892256
Dihydroceramide,3TBDMS,isomer #1CCCCCCCCCCCCCCC[C@@H](O[Si](C)(C)C(C)(C)C)[C@H](CO[Si](C)(C)C(C)(C)C)N(C=O)[Si](C)(C)C(C)(C)C3052.2Standard polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Dihydroceramide GC-MS (Non-derivatized) - 70eV, Positivesplash10-000l-9761000000-49c3e7ef71f565d78a202016-09-22Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dihydroceramide GC-MS (2 TMS) - 70eV, Positivesplash10-001i-2490200000-ce76ab5497791fd51fe62017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dihydroceramide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Dihydroceramide GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 10V, Positive-QTOFsplash10-0il0-0049000000-5dfda3f1388f3abf30f82016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 20V, Positive-QTOFsplash10-03ec-5396000000-450d57020d5338301d112016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 40V, Positive-QTOFsplash10-0007-4970000000-e72e84aaddbd263f496c2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 10V, Negative-QTOFsplash10-004i-2059000000-0a230b14683a27fa8d7b2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 20V, Negative-QTOFsplash10-01r7-9074000000-7b5c74746bfdd2286b682016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 40V, Negative-QTOFsplash10-002f-9010000000-dbf19cabd1b95226fa8d2016-09-14Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 10V, Positive-QTOFsplash10-001i-0009000000-9df513b3b35b71e705792021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 20V, Positive-QTOFsplash10-00lr-0059000000-57e37cdd69b1cdd2833b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 40V, Positive-QTOFsplash10-02u0-0094000000-e3d26a0a236ec35d2a652021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 10V, Negative-QTOFsplash10-004i-0009000000-ba73a2cbcbb544cfeda72021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 20V, Negative-QTOFsplash10-004i-0019000000-2e93209c7f8eb50ded102021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Dihydroceramide 40V, Negative-QTOFsplash10-002b-1096000000-3456b2e34beb0df0f5152021-09-23Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
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 IDFDB024056
KNApSAcK IDNot Available
Chemspider ID21436314
KEGG Compound IDC12126
BioCyc IDNot Available
BiGG ID2263543
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound16755624
PDB IDNot Available
ChEBI ID31488
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

Only showing the first 10 proteins. There are 68 proteins in total.

Enzymes

General function:
Involved in galactosylceramidase activity
Specific function:
Hydrolyzes the galactose ester bonds of galactosylceramide, galactosylsphingosine, lactosylceramide, and monogalactosyldiglyceride. Enzyme with very low activity responsible for the lysosomal catabolism of galactosylceramide, a major lipid in myelin, kidney and epithelial cells of small intestine and colon.
Gene Name:
GALC
Uniprot ID:
P54803
Molecular weight:
77062.86
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
Catalyzes the formation of some glycolipid via the addition of N-acetylgalactosamine (GalNAc) in alpha-1,3-linkage to some substrate. Glycolipids probably serve for adherence of some pathogens
Gene Name:
GBGT1
Uniprot ID:
Q8N5D6
Molecular weight:
40126.9
General function:
Involved in N-acetylglucosaminylphosphatidylinositol de
Specific function:
Involved in the second step of GPI biosynthesis. De-N-acetylation of N-acetylglucosaminyl-phosphatidylinositol.
Gene Name:
PIGL
Uniprot ID:
Q9Y2B2
Molecular weight:
28530.965
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Required for cell growth
Gene Name:
SGMS2
Uniprot ID:
Q8NHU3
Molecular weight:
42279.8
General function:
Involved in catalytic activity
Specific function:
Bidirectional lipid cholinephosphotransferase capable of converting phosphatidylcholine (PC) and ceramide to sphingomyelin (SM) and diacylglycerol (DAG) and vice versa. Direction is dependent on the relative concentrations of DAG and ceramide as phosphocholine acceptors. Directly and specifically recognizes the choline head group on the substrate. Also requires two fatty chains on the choline-P donor molecule in order to be recognized efficiently as a substrate. Does not function strictly as a SM synthase. Suppresses BAX-mediated apoptosis and also prevents cell death in response to stimuli such as hydrogen peroxide, osmotic stress, elevated temperature and exogenously supplied sphingolipids. May protect against cell death by reversing the stress-inducible increase in levels of proapoptotic ceramide. Required for cell growth
Gene Name:
SGMS1
Uniprot ID:
Q86VZ5
Molecular weight:
49207.3
General function:
Involved in hydrolase activity
Specific function:
Converts sphingomyelin to ceramide. Also has phospholipase C activities toward 1,2-diacylglycerolphosphocholine and 1,2-diacylglycerolphosphoglycerol. Isoform 2 and isoform 3 have lost catalytic activity.
Gene Name:
SMPD1
Uniprot ID:
P17405
Molecular weight:
69935.53
General function:
Cell wall/membrane/envelope biogenesis
Specific function:
Catalyzes the first glycosylation step in glycosphingolipid biosynthesis, the transfer of glucose to ceramide. May also serve as a "flippase".
Gene Name:
UGCG
Uniprot ID:
Q16739
Molecular weight:
44853.255
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltransferase activity
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGQ
Uniprot ID:
Q9BRB3
Molecular weight:
65343.25
General function:
Involved in biosynthetic process
Specific function:
Necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, the very early intermediate in GPI-anchor biosynthesis.
Gene Name:
PIGA
Uniprot ID:
P37287
Molecular weight:
54126.065
General function:
Involved in phosphatidylinositol N-acetylglucosaminyltr
Specific function:
Part of the complex catalyzing the transfer of N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol, the first step of GPI biosynthesis.
Gene Name:
PIGH
Uniprot ID:
Q14442
Molecular weight:
21080.415

Only showing the first 10 proteins. There are 68 proteins in total.