A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Berberine are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Berberine?

The molecule Berberine presents a molecular formula of C20H18NO4+ and its IUPAC name is 16,17-dimethoxy-5,7-dioxa-13-azoniapentacyclo[,10.04,8.015,20]henicosa-1(13),2,4(8),9,14,16,18,20-octaene.

Berberine is a molecule that has a wide range of potential health benefits. It belongs in the roots and bark of a number of different plants, including goldenseal, barberry, and Oregon grape. Berberine has been used in traditional Chinese medicine for centuries, and is now being studied for its potential to treat a variety of conditions..

Berberine has strong antimicrobial activity, and can be effective against a number of different bacteria, viruses, and fungi. It is also being studied for its potential to treat cancer. In addition, berberine has shown promise in treating diabetes, high cholesterol, and obesity..

While berberine has a wide range of potential health benefits, more research is needed to confirm its efficacy and safety. Berberine is generally well-tolerated, but can cause side effects such as nausea, vomiting, and diarrhea. It is important to speak with a healthcare provider before taking berberine, as it may interact with certain medications..

3D structure

Cartesian coordinates

Geometry of Berberine in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing


Berberine YBHILYKTIRIUTE-UHFFFAOYSA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name16,17-dimethoxy-5,7-dioxa-13-azoniapentacyclo[,10.04,8.015,20]henicosa-1(13),2,4(8),9,14,16,18,20-octaene
InChI codeInChI=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

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • 086B831
  • 0I8Y3P32UF
  • 16,17-dimethoxy-5,7-dioxa-13$l^{5}-azapentacyclo[^{2,10}.0^{4,8}.0^{15,20}]henicosa-1(13),2,4(8),9,14,16,18,20-octaen-13-ylium
  • 16,17-dimethoxy-5,7-dioxa-13-azoniapentacyclo[,10.04,8.015,20]henicosa-1(13),2,4(8),9,14,16,18,20-octaene
  • 2086-83-1
  • 3,4-dimethoxy-6,7-dihydro-[1,3]dioxolo[4,5-g]pyrido[2,1-a]isoquinolin-5-ylium
  • 3-[3-(2-ethyl-1,3-thiazol-4-yl)phenyl]-5-{2-[(4-methylphenyl)sulfonyl]ethyl}-1,2,4-oxadiazole
  • 34MD1011DM
  • 5,6-Dihydro-9,10-dimethoxybenzo[g]-1,3-benzodioxolo[5,6-a]quinolizinium
  • 5,6-dihydro-9,10-dimethoxy-benzo[g]-1,3-benzodioxolo[5,6-a]quinolizinium
  • 7,8,13,13a-tetradehydro-9,10-dimethoxy-2,3-(methylenedioxy)berbinium
  • 9,10-Dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetrahydroberbinium
  • 9,10-Dimethoxy-5,6-dihydro-7lambda~5~-[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinoline
  • 9,10-Dimethoxy-5,6-dihydro-[1,3]dioxolo-[4,5-g]isoquinolino[3,2-a]isoquinolin-7-ium
  • 9,10-Dimethoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ylium
  • 9,10-Dimethoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ylium chloride
  • 9,10-Dimethoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ylium; chloride
  • 9,10-Dimethoxy-5,6-dihydro-[1,3]dioxolo[4,5-g]isoquinolino[3,2-a]isoquinolin-7-ium
  • 9,10-dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbinium
  • 9,10-dimethoxy-5,6-dihydro[1,3]dioxolo[4,5-g]isoquino[3,2-a]isoquinolin-7-ium
  • A904183
  • AC-117
  • ACon1_001957
  • BBL029198
  • BCBcMAP01_000112
  • BDBM50203126
  • BER
  • BPBio1_000476
  • BRN 3570374
  • BSPBio_000432
  • BSPBio_002156
  • Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy-
  • Benzo[g]-1,3-benzodioxolo[5,6-a]quinolizinium, 5,6-dihydro-9,10-dimethoxy-
  • Benzo[g]-1,3-benzodioxolo[5,6-a]quinolizinium, 5,6-dihydro-9,10-dimethoxy- (9CI)
  • Benzylpenicillin benzathine, Antibiotic for Culture Media Use Only
  • Berbamine sulphate acid
  • Berberal
  • Berbericine
  • Berberin
  • Berberine
  • Berberine hydrogen sulfate
  • Berberone
  • Berbinium
  • Berbinium, 7,8,13,13a-tetradehydro-9,10-dimethoxy-2,3-(methylenedioxy)-
  • Berbinium, 7,8,13,13a-tetradehydro-9,10-dimethoxy-2,3-(methylenedioxy)-, chloride
  • C00757
  • C20H18NO4
  • CCG-35898
  • CS-0009734
  • Coptis rhizome
  • DB-050153
  • DB04115
  • DivK1c_000265
  • FT-0603587
  • GNF-PF-4545
  • GTPL11353
  • HMS3561D13
  • HY-N0716
  • IDI1_000265
  • KBio1_000265
  • KBio2_001590
  • KBio2_004158
  • KBio2_006726
  • KBio3_001656
  • KBioGR_001230
  • KBioSS_001590
  • MEGxp0_001923
  • Majarine
  • N1368
  • NCGC00016526-01
  • NCGC00016526-02
  • NCGC00016526-03
  • NCGC00016526-04
  • NCGC00016526-05
  • NCGC00016526-06
  • NCGC00016526-07
  • NCGC00016526-08
  • NCGC00016526-11
  • NCGC00091896-03
  • NCI60_001050
  • NCI60_001224
  • NCI60_004319
  • NCIMech_000354
  • NINDS_000265
  • NSC646666
  • Prestwick0_000586
  • Prestwick1_000586
  • Prestwick2_000586
  • Prestwick3_000586
  • Q-200701
  • Q-200702
  • Q176525
  • SBI-0051613.P002
  • SDCCGMLS-0066718.P001
  • SMP1_000298
  • SR-01000711827-5
  • ST055798
  • STK870320
  • Thalsine
  • Umbellatin
  • Umbellatine
  • Umbellatine (6CI)
  • berberine
  • berberine dimer
  • cid_12456
  • s9046

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC3779067
  • CAS-633-65-8
  • UNII-0I8Y3P32UF
  • AKOS002141363
  • BRD-K14796088-003-06-0
  • BRD-K14796088-003-17-7
  • DTXSID9043857
  • CHEMBL12089
  • CHEMBL295124
  • CHEBI:16118
  • EINECS 218-229-1
  • SPBio_000708
  • SPBio_002651
  • UPCMLD-DP032
  • UPCMLD-DP032:001
  • SCHEMBL25632
  • Spectrum_001110
  • Spectrum2_000894
  • Spectrum3_000618
  • Spectrum4_000785
  • Spectrum5_001458

Physico-Chemical properties

IUPAC name16,17-dimethoxy-5,7-dioxa-13-azoniapentacyclo[,10.04,8.015,20]henicosa-1(13),2,4(8),9,14,16,18,20-octaene
Molecular formulaC20H18NO4+
Molecular weight336.361
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity94.87
Topological polar surface area40.8

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.