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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 17:35:48 UTC
Update Date2022-03-07 02:52:29 UTC
HMDB IDHMDB0030266
Secondary Accession Numbers
  • HMDB30266
Metabolite Identification
Common NameBerberrubine
DescriptionBerberrubine, also known as 6847-93-4 or 9-berberoline, belongs to the class of organic compounds known as protoberberine alkaloids and derivatives. These are alkaloids with a structure based on a protoberberine moiety, which consists of a 5,6-dihydrodibenzene moiety fused to a quinolizinium and forming 5,6-Dihydrodibenzo(a,g)quinolizinium skeleton. Based on a literature review a significant number of articles have been published on Berberrubine.
Structure
Data?1563861962
Synonyms
ValueSource
6847-93-4HMDB
9-BerberolineHMDB
9-Berberoline chlorideHMDB
Berberrubine chlorideHMDB
5,6-Dihydro-9-hydroxy-10-methoxybenzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium chlorideHMDB
BerberrubineMeSH
Chemical FormulaC19H16NO4
Average Molecular Weight322.3346
Monoisotopic Molecular Weight322.107933005
IUPAC Name16-hydroxy-17-methoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15(20),16,18-octaen-13-ylium
Traditional Name16-hydroxy-17-methoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15(20),16,18-octaen-13-ylium
CAS Registry Number17388-19-1
SMILES
COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2
InChI Identifier
InChI=1S/C19H15NO4/c1-22-16-3-2-11-6-15-13-8-18-17(23-10-24-18)7-12(13)4-5-20(15)9-14(11)19(16)21/h2-3,6-9H,4-5,10H2,1H3/p+1
InChI KeyGLYPKDKODVRYGP-UHFFFAOYSA-O
Chemical Taxonomy
Description Belongs to the class of organic compounds known as protoberberine alkaloids and derivatives. These are alkaloids with a structure based on a protoberberine moiety, which consists of a 5,6-dihydrodibenzene moiety fused to a quinolizinium and forming 5,6-Dihydrodibenzo(a,g)quinolizinium skeleton.
KingdomOrganic compounds
Super ClassAlkaloids and derivatives
ClassProtoberberine alkaloids and derivatives
Sub ClassNot Available
Direct ParentProtoberberine alkaloids and derivatives
Alternative Parents
Substituents
  • Protoberberine skeleton
  • Isoquinoline
  • Benzodioxole
  • Anisole
  • Alkyl aryl ether
  • 1-hydroxy-4-unsubstituted benzenoid
  • Pyridine
  • Pyridinium
  • Benzenoid
  • Heteroaromatic compound
  • Acetal
  • Ether
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic nitrogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic cation
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water Solubility21.06 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.0028 g/LALOGPS
logP-0.31ALOGPS
logP-1.4ChemAxon
logS-5.3ALOGPS
pKa (Strongest Acidic)8.27ChemAxon
pKa (Strongest Basic)-4.5ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area51.8 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity89.04 m³·mol⁻¹ChemAxon
Polarizability34.9 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+179.40430932474
DeepCCS[M-H]-177.04630932474
DeepCCS[M-2H]-210.75630932474
DeepCCS[M+Na]+185.98330932474
AllCCS[M+H]+175.732859911
AllCCS[M+H-H2O]+172.432859911
AllCCS[M+NH4]+178.832859911
AllCCS[M+Na]+179.732859911
AllCCS[M-H]-183.032859911
AllCCS[M+Na-2H]-182.432859911
AllCCS[M+HCOO]-181.832859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
BerberrubineCOC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C24419.3Standard polar33892256
BerberrubineCOC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C22843.7Standard non polar33892256
BerberrubineCOC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C23367.3Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Berberrubine,1TMS,isomer #1COC1=CC=C2C=C3C4=CC5=C(C=C4CC[N+]3=CC2=C1O[Si](C)(C)C)OCO53228.4Semi standard non polar33892256
Berberrubine,1TBDMS,isomer #1COC1=CC=C2C=C3C4=CC5=C(C=C4CC[N+]3=CC2=C1O[Si](C)(C)C(C)(C)C)OCO53459.1Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Berberrubine GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fkc-0491000000-53e48c359255f28d48ca2017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Berberrubine 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 - Berberrubine 10V, Positive-QTOFsplash10-00di-0009000000-40ec3e631f941c5a27132016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 20V, Positive-QTOFsplash10-00di-0009000000-76ad903faa56ec5263942016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 40V, Positive-QTOFsplash10-0bt9-2293000000-e57d7291bbbcafda9e652016-06-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 10V, Negative-QTOFsplash10-00di-0009000000-dcf7ab775a1e5de918ad2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 20V, Negative-QTOFsplash10-00di-0009000000-e219118afc5ca46236ff2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 40V, Negative-QTOFsplash10-0ab9-6439000000-22e251b7c346e3e107c92016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 10V, Positive-QTOFsplash10-00di-0009000000-f52046137381c8e84ef02021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 20V, Positive-QTOFsplash10-00di-0029000000-b9911b2c91c3691094332021-09-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Berberrubine 40V, Positive-QTOFsplash10-024i-0092000000-a51b2504a55540662d4a2021-09-25Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-30Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB002095
KNApSAcK IDC00026111
Chemspider ID65548
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound72704
PDB IDNot Available
ChEBI ID441632
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1818521
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Park KD, Lee JH, Kim SH, Kang TH, Moon JS, Kim SU: Synthesis of 13-(substituted benzyl) berberine and berberrubine derivatives as antifungal agents. Bioorg Med Chem Lett. 2006 Aug 1;16(15):3913-6. Epub 2006 May 30. [PubMed:16730982 ]
  2. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .