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Record Information
Version4.0
StatusDetected and Quantified
Creation Date2006-08-12 20:17:34 UTC
Update Date2020-02-26 21:24:35 UTC
HMDB IDHMDB0003409
Secondary Accession Numbers
  • HMDB03409
Metabolite Identification
Common NameBerberine
DescriptionBerberine, also known as coptis rhizome, 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. Berberine is a quaternary ammonium salt from the protoberberine group of benzylisoquinoline alkaloids found in such plants as Berberis (e.g. Berberis vulgaris – barberry, Berberis aristata – tree turmeric, Mahonia aquifolium – Oregon-grape, Hydrastis canadensis – goldenseal, Xanthorhiza simplicissima – yellowroot, Phellodendron amurense – Amur cork tree, Coptis chinensis – Chinese goldthread, Tinospora cordifolia, Argemone mexicana – prickly poppy, and Eschscholzia californica – Californian poppy). As a natural dye, berberine has a color index of 75160. The alkaloid berberine has a tetracyclic skeleton derived from a benzyltetrahydroisoquinoline system with the incorporation of an extra carbon atom provided by S-adenosyl methionine via an N-methyl group. After oxidation and methylation by SAM, (S)-reticuline 4 is formed. This first recorded use of berberine is described in the ancient Chinese medical book The Divine Farmer's Herb-Root Classic. Berberine is a drug. Berberine is an extremely weak basic (essentially neutral) compound (based on its pKa). Berberine is a bitter tasting compound. L-DOPA and 4-hydroxypyruvic acid both come from L-tyrosine.
Structure
Data?1582752275
Synonyms
ValueSource
7,8,13,13a-Tetradehydro-9,10-dimethoxy-2,3-[methylenebis(oxy)]berbiniumChEBI
9,10-Dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbiniumChEBI
BerberinChEBI
Coptis rhizomeHMDB
Chemical FormulaC20H18NO4
Average Molecular Weight336.3612
Monoisotopic Molecular Weight336.123583069
IUPAC Name16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium
Traditional Name16,17-dimethoxy-5,7-dioxa-13lambda5-azapentacyclo[11.8.0.0^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium
CAS Registry Number2086-83-1
SMILES
COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC
InChI Identifier
InChI=1S/C20H18NO4/c1-22-17-4-3-12-7-16-14-9-19-18(24-11-25-19)8-13(14)5-6-21(16)10-15(12)20(17)23-2/h3-4,7-10H,5-6,11H2,1-2H3/q+1
InChI KeyYBHILYKTIRIUTE-UHFFFAOYSA-N
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
  • 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 Descriptors
Ontology
Disposition

Source:

Biological location:

Role

Industrial application:

Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point145 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
Water Solubility0.00035 g/LALOGPS
logP-0.18ALOGPS
logP-1.3ChemAxon
logS-6ALOGPS
pKa (Strongest Basic)-4.4ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.8 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity93.52 m³·mol⁻¹ChemAxon
Polarizability36.92 ųChemAxon
Number of Rings5ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0a4l-0059000000-2d03f2d248021273bb66Spectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-000i-0009000000-19928d40d547cbbc26dcSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-0029000000-42f72c3da8025ad70c4dSpectrum
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0103-0089000000-dbcf680bd232ed620a00Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-000i-0009000000-2993f75f22b9532dc39fSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-000i-0009000000-1d4cdb20920f8c900320Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-0079-0019000000-4995338b7526764bbad3Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-00dl-0059000000-ab35b8a7ec73f1063bb2Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-00fu-0089000000-09273e18fcd3186156f0Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-00di-0039000000-3a3f7eba3883c388e58cSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0006-0092000000-6f10979e1ecdd29611b1Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0006-0090000000-bacf940c54361560b64bSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITTOF (Shimadzu LC20A-IT-TOFMS) , Positivesplash10-000i-0009000000-3d6d1928f5797f4633e4Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITTOF (LCMS-IT-TOF) , Positivesplash10-000i-0009000000-6337ae6880e36d106adfSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00dl-0039000000-5d1ff6b7636484db90d1Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00dl-0059000000-131055c16d28a84b6130Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0009000000-9d8986d4bd9f3b6d634dSpectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-000i-0009000000-4459c8c8f7b607ad7b49Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00dr-0019000000-a0c1c55261d223b09256Spectrum
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00dl-0069000000-437bdc5509b367efef25Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0009000000-41bc0e7901cbc892051cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-000i-0009000000-b2e1ddadd60e4f52d2ddSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0iki-0179000000-85594d2e5f4b265077abSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0009000000-604df9f348201c3c531eSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0009000000-34b3c7d90696ff194395Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0nnc-3095000000-2e76003cd5b376964ba8Spectrum
1D NMR1H NMR SpectrumNot AvailableSpectrum
2D NMR[1H,13C] 2D NMR SpectrumNot AvailableSpectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biospecimen Locations
  • Blood
Tissue Locations
  • Fibroblasts
  • Intestine
  • Prostate
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected and Quantified0.0013 +/- 0.0012 uMAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB04115
Phenol Explorer Compound IDNot Available
FooDB IDFDB023165
KNApSAcK IDC00001819
Chemspider ID2263
KEGG Compound IDC00757
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBerberine
METLIN ID3471
PubChem Compound2353
PDB IDNot Available
ChEBI ID16118
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB ID
References
Synthesis ReferenceDominguez, Xorge A.; Garcia Delgado, Jesus; Reeves, Wylie P.; Gardner, Pete D. Photochemical formation of berberine alkaloids from protopine alkaloids. Tetrahedron Letters (1967), (26), 2493-5.
Material Safety Data Sheet (MSDS)Download (PDF)
General References
  1. Pan GY, Wang GJ, Sun JG, Huang ZJ, Zhao XC, Gu Y, Liu XD: [Inhibitory action of berberine on glucose absorption]. Yao Xue Xue Bao. 2003 Dec;38(12):911-4. [PubMed:15040083 ]
  2. Yu HH, Kim KJ, Cha JD, Kim HK, Lee YE, Choi NY, You YO: Antimicrobial activity of berberine alone and in combination with ampicillin or oxacillin against methicillin-resistant Staphylococcus aureus. J Med Food. 2005 Winter;8(4):454-61. [PubMed:16379555 ]
  3. Zhao CC, Zheng WF, Li MQ: [The interaction of berberine and human serum albumin]. Guang Pu Xue Yu Guang Pu Fen Xi. 2004 Jan;24(1):111-3. [PubMed:15768991 ]
  4. Pan JF, Yu C, Zhu DY, Zhang H, Zeng JF, Jiang SH, Ren JY: Identification of three sulfate-conjugated metabolites of berberine chloride in healthy volunteers' urine after oral administration. Acta Pharmacol Sin. 2002 Jan;23(1):77-82. [PubMed:11860742 ]
  5. Zhang H, Shao Z, Sun Y: [Determination of berberine in human serum by reversed-phase high performance liquid chromatography]. Se Pu. 1997 Sep;15(5):454-5. [PubMed:15739507 ]
  6. Liu Y, Huang CZ, Li YF: Fluorescence assay based on preconcentration by a self-ordered ring using berberine as a model analyte. Anal Chem. 2002 Nov 1;74(21):5564-8. [PubMed:12433089 ]
  7. Mantena SK, Sharma SD, Katiyar SK: Berberine, a natural product, induces G1-phase cell cycle arrest and caspase-3-dependent apoptosis in human prostate carcinoma cells. Mol Cancer Ther. 2006 Feb;5(2):296-308. [PubMed:16505103 ]