Hmdb loader
Survey
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 Date2012-09-11 23:25:12 UTC
Update Date2022-03-07 02:55:38 UTC
HMDB IDHMDB0038137
Secondary Accession Numbers
  • HMDB38137
Metabolite Identification
Common NameBicyclogermacrene
DescriptionBicyclogermacrene belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]undecane, 9CI) skeleton or the isolepidozane skeleton. Based on a literature review a significant number of articles have been published on Bicyclogermacrene.
Structure
Data?1563863145
Synonyms
ValueSource
N(6)-(N-Threonylcarbonyl)adenosineHMDB
Chemical FormulaC15H24
Average Molecular Weight204.3511
Monoisotopic Molecular Weight204.187800768
IUPAC Name(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene
Traditional Name(2Z,6Z)-3,7,11,11-tetramethylbicyclo[8.1.0]undeca-2,6-diene
CAS Registry Number24703-35-3
SMILES
C\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C
InChI Identifier
InChI=1S/C15H24/c1-11-6-5-7-12(2)10-14-13(9-8-11)15(14,3)4/h6,10,13-14H,5,7-9H2,1-4H3/b11-6-,12-10-
InChI KeyVPDZRSSKICPUEY-SUYBHAEQSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as bicyclogermacrane and isolepidozane sesquiterpenoids. These are sesquiterpenoids with a structure based either on the bicyclogermacrane (3,7,11,11-tetramethylbicyclo[8.1.0]Undecane, 9CI) skeleton or the isolepidozane skeleton.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassSesquiterpenoids
Direct ParentBicyclogermacrane and isolepidozane sesquiterpenoids
Alternative Parents
Substituents
  • Bicyclogermacrane sesquiterpenoid
  • Branched unsaturated hydrocarbon
  • Polycyclic hydrocarbon
  • Cyclic olefin
  • Unsaturated aliphatic hydrocarbon
  • Unsaturated hydrocarbon
  • Olefin
  • Hydrocarbon
  • Aliphatic homopolycyclic compound
Molecular FrameworkAliphatic homopolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Disposition
Process
Role
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling Point267.00 to 268.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility0.058 mg/L @ 25 °C (est)The Good Scents Company Information System
LogP6.498 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0084 g/LALOGPS
logP5.09ALOGPS
logP4.46ChemAxon
logS-4.4ALOGPS
Physiological Charge0ChemAxon
Hydrogen Acceptor Count0ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area0 ŲChemAxon
Rotatable Bond Count0ChemAxon
Refractivity68.52 m³·mol⁻¹ChemAxon
Polarizability25.91 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+148.51831661259
DarkChem[M-H]-146.18731661259
DeepCCS[M+H]+158.59830932474
DeepCCS[M-H]-156.2430932474
DeepCCS[M-2H]-189.17230932474
DeepCCS[M+Na]+164.69130932474
AllCCS[M+H]+146.332859911
AllCCS[M+H-H2O]+142.332859911
AllCCS[M+NH4]+150.132859911
AllCCS[M+Na]+151.232859911
AllCCS[M-H]-156.432859911
AllCCS[M+Na-2H]-156.932859911
AllCCS[M+HCOO]-157.532859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
BicyclogermacreneC\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C1683.9Standard polar33892256
BicyclogermacreneC\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C1465.3Standard non polar33892256
BicyclogermacreneC\C1=C\CC\C(C)=C/C2C(CC1)C2(C)C1486.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Bicyclogermacrene GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-1900000000-df419c5498786a94c8f42017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Bicyclogermacrene GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Bicyclogermacrene 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 - Bicyclogermacrene 10V, Positive-QTOFsplash10-0a4i-0290000000-216638dbc9bcc0fef59d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Positive-QTOFsplash10-0a4i-3950000000-79ba6cb8f3b30df6ad422016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Positive-QTOFsplash10-014i-9700000000-3a75cef7802fad80da522016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Negative-QTOFsplash10-0udi-0090000000-9b6e63803a1d9e7a723d2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Negative-QTOFsplash10-0udi-0390000000-00526b8f3a27bdd8e0992016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Negative-QTOFsplash10-01y9-1900000000-54c856e9a961651a0cfe2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Negative-QTOFsplash10-0udi-0090000000-7ccf03fa1149a1e9f55f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Negative-QTOFsplash10-0udi-0090000000-7ccf03fa1149a1e9f55f2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Negative-QTOFsplash10-0udi-0090000000-0b1ac00c3b3c6c0a73b92021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 10V, Positive-QTOFsplash10-0a4i-0190000000-695c9202804f5c6577ea2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 20V, Positive-QTOFsplash10-0a4i-0490000000-8ad2959b26bbbbcf295b2021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Bicyclogermacrene 40V, Positive-QTOFsplash10-0006-8900000000-80e416b8aa432948f8ed2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • 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 IDFDB017365
KNApSAcK IDC00012425
Chemspider ID20119973
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkGermacrene
METLIN IDNot Available
PubChem Compound21159022
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1551871
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.