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Record Information
Creation Date2006-08-12 20:17:34 UTC
Update Date2017-03-02 21:27:17 UTC
Secondary Accession NumbersNone
Metabolite Identification
Common NameBerberine
DescriptionBerberine is an alkaloid from Hydrastis canadensis L., Berberidaceae. It is also found in many other plants. It is relatively toxic parenterally, but has been used orally for various parasitic and fungal infections and as antidiarrheal.
Coptis rhizomeHMDB
Chemical FormulaC20H18NO4
Average Molecular Weight336.3612
Monoisotopic Molecular Weight336.123583069
IUPAC Name16,17-dimethoxy-5,7-dioxa-13λ⁵-azapentacyclo[²,¹⁰.0⁴,⁸.0¹⁵,²⁰]henicosa-1(21),2,4(8),9,13,15,17,19-octaen-13-ylium
Traditional Nameberberine
CAS Registry Number2086-83-1
InChI Identifier
Chemical Taxonomy
DescriptionThis compound belongs to the class of chemical entities 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.
KingdomChemical entities
Super ClassOrganic compounds
ClassAlkaloids and derivatives
Sub ClassProtoberberine alkaloids and derivatives
Direct ParentProtoberberine alkaloids and derivatives
Alternative Parents
  • 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
StatusDetected and Quantified
  • Drug
  • Plant
BiofunctionNot Available
ApplicationNot Available
Cellular locations
  • Membrane (predicted from logP)
Physical Properties
Experimental Properties
Melting Point145 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
Water Solubility0.000354 mg/mLALOGPS
pKa (Strongest Basic)-4.4ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area40.8 Å2ChemAxon
Rotatable Bond Count2ChemAxon
Refractivity93.52 m3·mol-1ChemAxon
Polarizability36.92 Å3ChemAxon
Number of Rings5ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Spectrum TypeDescriptionSplash Key
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-000i-0009000000-19928d40d547cbbc26dcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-00di-0029000000-42f72c3da8025ad70c4dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-0103-0089000000-dbcf680bd232ed620a00View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positivesplash10-000i-0009000000-2993f75f22b9532dc39fView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positivesplash10-000i-0009000000-1d4cdb20920f8c900320View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positivesplash10-0079-0019000000-4995338b7526764bbad3View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positivesplash10-00dl-0059000000-ab35b8a7ec73f1063bb2View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positivesplash10-00fu-0089000000-09273e18fcd3186156f0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-00di-0039000000-3a3f7eba3883c388e58cView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0006-0092000000-6f10979e1ecdd29611b1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positivesplash10-0006-0090000000-bacf940c54361560b64bView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITTOF (Shimadzu LC20A-IT-TOFMS) , Positivesplash10-000i-0009000000-3d6d1928f5797f4633e4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITTOF (LCMS-IT-TOF) , Positivesplash10-000i-0009000000-6337ae6880e36d106adfView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00dl-0039000000-5d1ff6b7636484db90d1View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QTOF , positivesplash10-00dl-0059000000-131055c16d28a84b6130View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-0009000000-9d8986d4bd9f3b6d634dView in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-0009000000-4459c8c8f7b607ad7b49View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00dr-0019000000-a0c1c55261d223b09256View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-00dl-0069000000-437bdc5509b367efef25View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-QQ , positivesplash10-000i-0009000000-7308f7a2cd31283860f7View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-00dr-0019000000-60003f93e70ee242f1c4View in MoNA
LC-MS/MSLC-MS/MS Spectrum - LC-ESI-ITFT , positivesplash10-00di-0019000000-14f0c8e22b0bd2c71ed0View in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-00di-0019000000-390bf95ccd98952a4dbcView in MoNA
LC-MS/MSLC-MS/MS Spectrum - , positivesplash10-00di-0019000000-62c2ee4b84c5aed05853View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
Biofluid Locations
  • Blood
Tissue Location
  • Fibroblasts
  • Intestine
  • Prostate
PathwaysNot Available
Normal Concentrations
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 IDNot Available
DrugBank Metabolite IDNot Available
Phenol Explorer Compound IDNot Available
Phenol Explorer Metabolite IDNot Available
FoodDB IDFDB023165
KNApSAcK IDNot Available
Chemspider ID2263
KEGG Compound IDC00757
BiGG IDNot Available
Wikipedia LinkBerberine
NuGOwiki LinkHMDB03409
Metagene LinkHMDB03409
PubChem Compound2353
ChEBI ID16118
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 ]