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Record Information
StatusExpected but not Quantified
Creation Date2012-09-11 17:38:24 UTC
Update Date2022-03-07 02:52:39 UTC
Secondary Accession Numbers
  • HMDB30682
Metabolite Identification
Common NameCubebin
DescriptionCubebin is found in herbs and spices. Cubebin is isolated from unripe fruit of Piper cubeba (cubeb pepper) About 15% of a volatile oil is obtained by distilling cubebs with water. Cubebene, the liquid portion, has the formula C15H24. It is a pale green or blue-yellow viscous liquid with a warm woody, slightly camphoraceous odor. After rectification with water, or on keeping, this deposits rhombic crystals of camphor of cubebs. Cubeb (Piper cubeba), or tailed pepper, is a plant in genus Piper, cultivated for its fruit and essential oil. It is mostly grown in Java and Sumatra, hence sometimes called Java pepper. The fruits are gathered before they are ripe, and carefully dried. Commercial cubebs consist of the dried berries, similar in appearance to black pepper, but with stalks attached the "tails" in "tailed pepper". The dried pericarp is wrinkled, its color ranges from grayish-brown to black. The seed is hard, white and oily. The odor of cubebs is described as agreeable and aromatic. The taste, pungent, acrid, slightly bitter and persistent. It has been described as tasting like allspice, or like a cross between allspice and black pepper. Cubebin (C10H10O3) is a crystalline substance existing in cubebs, discovered by Eugene Soubeiran and Capitaine in 1839. It may be prepared from cubebene, or from the pulp left after the distillation of the oil. The drug, along with gum, fatty oils, and malates of magnesium and calcium, contains also about 1% of cubebic acid, and about 6% of a resin. The dose of the fruit is 30 to 60 grains, and the British Pharmacopoeia contains a tincture with a dose of 4 to 1 dram. In Europe, cubeb was one of the valuable spices during the Middle Ages. It was ground as a seasoning for meat or used in sauces. Cubebin is a medieval recipe includes cubeb in making sauce sarcenes, which consists of almond milk and several spices. As an aromatic confectionery, cubeb was often candied and eaten whole. In traditional Chinese medicine cubeb is used for its alleged warming property. In Tibetan medicine, cubeb (ka ko la in Tibetan) is one of bzang po drug, six fine herbs beneficial to specific organs in the body, with cubeb assigned to the spleen
3,4-Bis(1,3-benzodioxol-5-ylmethyl)tetrahydro-2-furanol, 9ciHMDB
Chemical FormulaC20H20O6
Average Molecular Weight356.3692
Monoisotopic Molecular Weight356.125988372
IUPAC Name3,4-bis(2H-1,3-benzodioxol-5-ylmethyl)oxolan-2-ol
Traditional Name3,4-bis(2H-1,3-benzodioxol-5-ylmethyl)oxolan-2-ol
CAS Registry Number18423-69-3
InChI Identifier
Chemical Taxonomy
Description Belongs to the class of organic compounds known as dibenzylbutyrolactols. These are lignan compounds containing a 3,4-dibenzyloxolan-2-ol moiety.
KingdomOrganic compounds
Super ClassLignans, neolignans and related compounds
ClassFuranoid lignans
Sub ClassTetrahydrofuran lignans
Direct ParentDibenzylbutyrolactols
Alternative Parents
  • Dibenzylbutyrolactol
  • Benzodioxole
  • Benzenoid
  • Tetrahydrofuran
  • Hemiacetal
  • Oxacycle
  • Organoheterocyclic compound
  • Acetal
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Physiological effectNot Available
ProcessNot Available
RoleNot Available
Physical Properties
Experimental Molecular Properties
Melting Point131 - 132 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Water Solubility0.047 g/LALOGPS
pKa (Strongest Acidic)12.17ChemAxon
pKa (Strongest Basic)-4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area66.38 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity91.51 m³·mol⁻¹ChemAxon
Polarizability36.44 ųChemAxon
Number of Rings5ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference

Predicted Kovats Retention Indices


MetaboliteSMILESKovats RI ValueColumn TypeReference
CubebinOC1OCC(CC2=CC3=C(OCO3)C=C2)C1CC1=CC2=C(OCO2)C=C14056.8Standard polar33892256
CubebinOC1OCC(CC2=CC3=C(OCO3)C=C2)C1CC1=CC2=C(OCO2)C=C12765.0Standard non polar33892256
CubebinOC1OCC(CC2=CC3=C(OCO3)C=C2)C1CC1=CC2=C(OCO2)C=C12994.7Semi standard non polar33892256


Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Cubebin,1TMS,isomer #1C[Si](C)(C)OC1OCC(CC2=CC=C3OCOC3=C2)C1CC1=CC=C2OCOC2=C12929.5Semi standard non polar33892256
Cubebin,1TBDMS,isomer #1CC(C)(C)[Si](C)(C)OC1OCC(CC2=CC=C3OCOC3=C2)C1CC1=CC=C2OCOC2=C13174.7Semi standard non polar33892256

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Cubebin GC-MS (Non-derivatized) - 70eV, Positivesplash10-009i-1339000000-11a72c1bb579684dd2382017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cubebin GC-MS (1 TMS) - 70eV, Positivesplash10-007c-9355200000-58b9915031467f1e363d2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Cubebin 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 - Cubebin 10V, Positive-QTOFsplash10-0a4i-0139000000-dbdae8d0ed784a64a8a92016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 20V, Positive-QTOFsplash10-08g1-0869000000-a57842f4225a1d634d0a2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 40V, Positive-QTOFsplash10-0f6t-0930000000-e6b6af605b413e476adc2016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 10V, Negative-QTOFsplash10-0a4i-0009000000-56cf92cfc1408e7d6be92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 20V, Negative-QTOFsplash10-0a4i-0019000000-881571ceb71f68ef248b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 40V, Negative-QTOFsplash10-0005-1492000000-69b828ecf7edce8dc2c32016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 10V, Positive-QTOFsplash10-0a4i-0019000000-b2bea62dd56524b65bac2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 20V, Positive-QTOFsplash10-0550-0119000000-04bae9b44cac90ee82fb2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 40V, Positive-QTOFsplash10-06ri-0729000000-25e25a08e8016a60024e2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 10V, Negative-QTOFsplash10-0a4i-0009000000-7442d31f4cb7b9cb1e502021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 20V, Negative-QTOFsplash10-0a6r-0019000000-4a7ed918e3b1fceb0bd42021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Cubebin 40V, Negative-QTOFsplash10-0np4-2359000000-a28c20569adca690a7e52021-09-22Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
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 IDFDB002600
KNApSAcK IDC00002591
Chemspider ID253695
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkPiper cubeba
METLIN IDNot Available
PubChem Compound287685
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Borsato ML, Grael CF, Souza GE, Lopes NP: Analgesic activity of the lignans from Lychnophora ericoides. Phytochemistry. 2000 Dec;55(7):809-13. [PubMed:11190401 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .