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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 21:51:27 UTC
Update Date2022-03-07 02:55:01 UTC
HMDB IDHMDB0036691
Secondary Accession Numbers
  • HMDB36691
Metabolite Identification
Common Name3-Dehydronobilin
Description3-Dehydronobilin belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety. Based on a literature review a significant number of articles have been published on 3-Dehydronobilin.
Structure
Data?1563862910
Synonyms
ValueSource
6,10-Dimethyl-3-methylidene-2,9-dioxo-2H,3H,3ah,4H,5H,8H,9H,11ah-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoic acidHMDB
Chemical FormulaC20H24O5
Average Molecular Weight344.4016
Monoisotopic Molecular Weight344.162373878
IUPAC Name6,10-dimethyl-3-methylidene-2,9-dioxo-2H,3H,3aH,4H,5H,8H,9H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate
Traditional Name6,10-dimethyl-3-methylidene-2,9-dioxo-3aH,4H,5H,8H,11aH-cyclodeca[b]furan-4-yl (2Z)-2-methylbut-2-enoate
CAS Registry Number63529-14-6
SMILES
C\C=C(\C)C(=O)OC1C\C(C)=C\CC(=O)\C(C)=C\C2OC(=O)C(=C)C12
InChI Identifier
InChI=1S/C20H24O5/c1-6-12(3)19(22)24-16-9-11(2)7-8-15(21)13(4)10-17-18(16)14(5)20(23)25-17/h6-7,10,16-18H,5,8-9H2,1-4H3/b11-7+,12-6-,13-10+
InChI KeyFKDIIXZIKCNXAT-QLDBJWRKSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as germacranolides and derivatives. These are sesquiterpene lactones with a structure based on the germacranolide skeleton, characterized by a gamma lactone fused to a 1,7-dimethylcyclodec-1-ene moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene lactones
Direct ParentGermacranolides and derivatives
Alternative Parents
Substituents
  • Germacranolide
  • Germacrane sesquiterpenoid
  • Sesquiterpenoid
  • Fatty acid ester
  • Dicarboxylic acid or derivatives
  • Gamma butyrolactone
  • Fatty acyl
  • Alpha,beta-unsaturated carboxylic ester
  • Tetrahydrofuran
  • Enoate ester
  • Lactone
  • Ketone
  • Carboxylic acid ester
  • Cyclic ketone
  • Organoheterocyclic compound
  • Oxacycle
  • Carboxylic acid derivative
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Carbonyl group
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Process
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point205 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility14.57 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.023 g/LALOGPS
logP3.19ALOGPS
logP4.02ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)6.17ChemAxon
pKa (Strongest Basic)-5.8ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area69.67 ŲChemAxon
Rotatable Bond Count3ChemAxon
Refractivity96.04 m³·mol⁻¹ChemAxon
Polarizability35.76 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M-2H]-220.21730932474
DeepCCS[M+Na]+195.4230932474
AllCCS[M+H]+184.332859911
AllCCS[M+H-H2O]+181.332859911
AllCCS[M+NH4]+187.032859911
AllCCS[M+Na]+187.832859911
AllCCS[M-H]-187.332859911
AllCCS[M+Na-2H]-187.532859911
AllCCS[M+HCOO]-187.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-DehydronobilinC\C=C(\C)C(=O)OC1C\C(C)=C\CC(=O)\C(C)=C\C2OC(=O)C(=C)C123705.8Standard polar33892256
3-DehydronobilinC\C=C(\C)C(=O)OC1C\C(C)=C\CC(=O)\C(C)=C\C2OC(=O)C(=C)C122573.2Standard non polar33892256
3-DehydronobilinC\C=C(\C)C(=O)OC1C\C(C)=C\CC(=O)\C(C)=C\C2OC(=O)C(=C)C122628.8Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
3-Dehydronobilin,1TMS,isomer #1C=C1C(=O)OC2/C=C(C)/C(O[Si](C)(C)C)=C/C=C(\C)CC(OC(=O)/C(C)=C\C)C122846.6Semi standard non polar33892256
3-Dehydronobilin,1TMS,isomer #1C=C1C(=O)OC2/C=C(C)/C(O[Si](C)(C)C)=C/C=C(\C)CC(OC(=O)/C(C)=C\C)C122406.8Standard non polar33892256
3-Dehydronobilin,1TBDMS,isomer #1C=C1C(=O)OC2/C=C(C)/C(O[Si](C)(C)C(C)(C)C)=C/C=C(\C)CC(OC(=O)/C(C)=C\C)C123053.5Semi standard non polar33892256
3-Dehydronobilin,1TBDMS,isomer #1C=C1C(=O)OC2/C=C(C)/C(O[Si](C)(C)C(C)(C)C)=C/C=C(\C)CC(OC(=O)/C(C)=C\C)C122575.2Standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Dehydronobilin GC-MS (Non-derivatized) - 70eV, Positivesplash10-0kai-9032000000-275d5fb73e9f5ca7a0f02017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Dehydronobilin 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 - 3-Dehydronobilin 10V, Positive-QTOFsplash10-0002-3059000000-ddaab2f0dd2ef979b9132016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 20V, Positive-QTOFsplash10-0032-9152000000-2501bf40adf2334fad3a2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 40V, Positive-QTOFsplash10-0fsi-9210000000-16b49fceac282eb89e4c2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 10V, Negative-QTOFsplash10-0006-1049000000-3c3fa14a3682f10714752016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 20V, Negative-QTOFsplash10-0005-6096000000-a1b30547b95e9219cb082016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 40V, Negative-QTOFsplash10-001a-9430000000-9abec1ed0dd653fa37202016-08-04Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 10V, Positive-QTOFsplash10-0002-0090000000-7bd2870eed539375aefa2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 20V, Positive-QTOFsplash10-0002-1190000000-bc266add0e756f89201a2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 40V, Positive-QTOFsplash10-00os-3190000000-7392f9be87fed855c0182021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 10V, Negative-QTOFsplash10-0005-9065000000-b15016ab15342df11caf2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 20V, Negative-QTOFsplash10-0002-9040000000-dc0ad5f590e8391f04fd2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Dehydronobilin 40V, Negative-QTOFsplash10-0pb9-9050000000-ec0e5a17ba1a1ad5ff392021-09-24Wishart 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 IDFDB015623
KNApSAcK IDC00011800
Chemspider ID35014203
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound131752038
PDB IDNot Available
ChEBI ID174642
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1856501
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.