NP-MRD: Showing NP-Card for Berberine (NP0000008)

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Record Information

Version

1.0

Created at

2006-08-12 20:17:34 UTC

Updated at

2021-08-19 20:22:28 UTC

NP-MRD ID

NP0000008

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Berberine

Description

Berberine is a quaternary ammonium salt that belongs to the protoberberine group of benzylisoquinoline alkaloids. Chemically, berberine is classified as an isoquinoline alkaloid. More specifically, berberine is a plant alkaloid derived from tyrosine through a complex 8 step biosynthetic process. Berberine is found in plants such as Berberis vulgaris (barberry), Berberis aristata (tree turmeric), Mahonia aquifolium (Oregon grape) and Hydrastis canadensis (goldenseal). Two other known berberine-containing plants are Phellodendron chinense and Phellodendron amurense. Berberine is usually found in the roots, rhizomes, stems, and bark of Berberis plants. Due to berberine's intense yellow color, plants that contain berberine were traditionally used to dye wool, leather, and wood. Under ultraviolet light, berberine shows a strong yellow fluorescence, making it useful in histology for staining heparin in mast cells. Berberine is a bioactive plant compound that has been frequently used in traditional medicine. Among the known physiological effects or bioactivities are: 1) Antimicrobial action against bacteria, fungi, protozoa, viruses, helminthes, and Chlamydia; 2) Antagonism against the effects of cholera and E coli heat-stable enterotoxin; 3) Inhibition of intestinal ion secretion and of smooth muscle contraction; 4) Reduction of inflammation and 5) Stimulation of bile secretion and bilirubin discharge (PMID: 32335802 ). Berberine can inhibit bacterial growth in the gut, including Helicobacter pylori, protect the intestinal epithelial barrier from injury, and ameliorate liver injury. Currently, berberine is sold as an Over-the-Counter (OTC) drug for treating gastrointestinal infections in China (PMID: 18442638 ). Berberine also inhibits the proliferation of various types of cancer cells and impedes invasion and metastasis (PMID: 32335802 ). Recent evidence has also confirmed that berberine improves the efficacy and safety of both chemo and radiotherapies for cancer treatment (PMID: 32335802 ). Berberine has also been shown to regulate glucose and lipid metabolism in vitro and in vivo (PMID: 18442638 ). In fact, berberine is the main active component of an ancient Chinese herb Coptis chinensis French, which has been used to treat diabetes for thousands of years. As an anti-diabetic, berberine increases glucose uptake by muscle fibers independent of insulin levels. It triggers AMPK activation and increases glycolysis, leading to decreased insulin resistance and decreased oxygen respiration. The same mechanism leads to a reduction in gluconeogenesis in the liver. AMPK activation by berberine also leads to an antiatherosclerotic effect in mice. Berberine's AMPK activation may also underlie berberines' anti-obesity effects and favorable influence on weight loss (PMID: 18442638 ). While its use as a medication is widely touted, it is important to remember that berberine inhibits CYP2D6 and CYP3A4 enzymes, both of which are involved in the metabolism of many endogenous substances and xenobiotics, including a number of prescription drugs.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI


  Mrv1652305201900032D          

 25 29  0  0  0  0            999 V2000
   -2.0514   -4.0458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -3.3251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249   -3.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4233   -2.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4016   -2.5793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249   -3.2875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6498   -3.2749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0731   -3.9830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8980   -3.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2996   -3.2498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1245   -3.2373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5478   -3.9454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3521   -3.7616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4259   -2.9399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6672   -2.6158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1463   -4.6660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3213   -4.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9198   -5.3993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0949   -5.4118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6715   -4.7037    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8466   -4.7162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4233   -4.0081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4016   -4.0207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8032   -4.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -4.7539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  2  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  8 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  2  0  0  0  0
  3 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
M  CHG  1  20   1
M  END

HMDB0003409
     RDKit          3D
Berberine
 43 47  0  0  0  0  0  0  0  0999 V2000
   -5.0207    4.0731   -0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6121    2.8063   -0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3354    2.3522   -0.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4647    3.1265    0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1881    2.6629    0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7876    1.4296    0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881    0.9148    0.4024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8776   -0.3205   -0.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0538   -1.0903   -0.7898 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1993   -0.5861   -1.0384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6290    0.6334   -0.5932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8963    1.1249   -0.8544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7407    0.3329   -1.5947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5751   -0.5824   -0.9298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3768   -2.3557   -1.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5389   -3.0508   -0.8057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5089   -2.1636   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8089   -2.6067    0.1148 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7283   -1.8266    0.7788 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3901   -0.5608    1.1975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1058   -0.1076    0.9271 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1780   -0.9022    0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722    0.0075    1.8313 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2755   -1.1031    2.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0560   -2.0060    1.1800 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8422    4.1550    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4527    4.8882   -0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1093    4.2086   -0.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7907    4.1043    0.6949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    3.2883    1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1143    1.5623    0.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8946   -1.1768   -1.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2736   -1.0315   -1.6659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2002   -0.1262   -0.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9839   -1.3788   -0.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5919   -2.1808   -2.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5461   -3.0311   -1.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2260   -3.8887   -0.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0476   -3.6075   -1.6673 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0585   -3.5855   -0.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8289    0.8658    1.2418 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3562   -0.8030    2.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9908   -1.4895    3.2246 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
  9 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 20 23  1  0
 23 24  1  0
 24 25  1  0
 12  3  1  0
 22 17  1  0
 11  6  1  0
 25 19  1  0
 22  8  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 18 40  1  0
 21 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  1   9   1
M  END


  Mrv1652305201900032D          

 25 29  0  0  0  0            999 V2000
   -2.0514   -4.0458    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -3.3251    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8249   -3.3125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4233   -2.5919    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4016   -2.5793    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8249   -3.2875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6498   -3.2749    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0731   -3.9830    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8980   -3.9705    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2996   -3.2498    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1245   -3.2373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5478   -3.9454    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3521   -3.7616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4259   -2.9399    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6672   -2.6158    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1463   -4.6660    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3213   -4.6786    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9198   -5.3993    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0949   -5.4118    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6715   -4.7037    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    0.8466   -4.7162    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4233   -4.0081    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4016   -4.0207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8032   -4.7413    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6281   -4.7539    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 11 15  1  0  0  0  0
 12 16  1  0  0  0  0
 16 17  2  0  0  0  0
  9 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
  8 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
  6 22  1  0  0  0  0
 22 23  2  0  0  0  0
  3 23  1  0  0  0  0
 23 24  1  0  0  0  0
 24 25  1  0  0  0  0
M  CHG  1  20   1
M  END
> <DATABASE_ID>
NP0000008

> <DATABASE_NAME>
NP-MRD

> <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_KEY>
YBHILYKTIRIUTE-UHFFFAOYSA-N

> <FORMULA>
C20H18NO4

> <MOLECULAR_WEIGHT>
336.3612

> <EXACT_MASS>
336.123583069

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
43

> <JCHEM_AVERAGE_POLARIZABILITY>
36.919095262495745

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
16,17-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

> <ALOGPS_LOGP>
-0.18

> <JCHEM_LOGP>
-1.2833122858050783

> <ALOGPS_LOGS>
-6.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
-4.3828748310453145

> <JCHEM_POLAR_SURFACE_AREA>
40.8

> <JCHEM_REFRACTIVITY>
93.52329999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.54e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
16,17-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

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0003409
     RDKit          3D
Berberine
 43 47  0  0  0  0  0  0  0  0999 V2000
   -5.0207    4.0731   -0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6121    2.8063   -0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3354    2.3522   -0.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4647    3.1265    0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1881    2.6629    0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7876    1.4296    0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881    0.9148    0.4024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8776   -0.3205   -0.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0538   -1.0903   -0.7898 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1993   -0.5861   -1.0384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6290    0.6334   -0.5932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8963    1.1249   -0.8544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7407    0.3329   -1.5947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5751   -0.5824   -0.9298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3768   -2.3557   -1.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5389   -3.0508   -0.8057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5089   -2.1636   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8089   -2.6067    0.1148 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7283   -1.8266    0.7788 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3901   -0.5608    1.1975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1058   -0.1076    0.9271 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1780   -0.9022    0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722    0.0075    1.8313 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2755   -1.1031    2.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0560   -2.0060    1.1800 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8422    4.1550    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4527    4.8882   -0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1093    4.2086   -0.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7907    4.1043    0.6949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    3.2883    1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1143    1.5623    0.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8946   -1.1768   -1.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2736   -1.0315   -1.6659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2002   -0.1262   -0.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9839   -1.3788   -0.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5919   -2.1808   -2.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5461   -3.0311   -1.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2260   -3.8887   -0.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0476   -3.6075   -1.6673 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0585   -3.5855   -0.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8289    0.8658    1.2418 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3562   -0.8030    2.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9908   -1.4895    3.2246 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
  9 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 20 23  1  0
 23 24  1  0
 24 25  1  0
 12  3  1  0
 22 17  1  0
 11  6  1  0
 25 19  1  0
 22  8  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 18 40  1  0
 21 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  1   9   1
M  END

HEADER    PROTEIN                                 20-MAY-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-MAY-19         0                                  
HETATM    1  C   UNK     0      -3.829  -7.552   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -3.080  -6.207   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.540  -6.183   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.790  -4.838   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.750  -4.815   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.540  -6.137   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       3.080  -6.113   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       3.870  -7.435   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.410  -7.412   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.159  -6.066   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       7.699  -6.043   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.489  -7.365   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0       9.991  -7.022   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      10.128  -5.488   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0       8.712  -4.883   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0       7.740  -8.710   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       6.200  -8.733   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       5.450 -10.079   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.910 -10.102   0.000  0.00  0.00           C+0
HETATM   20  N   UNK     0       3.120  -8.780   0.000  0.00  0.00           N+1
HETATM   21  C   UNK     0       1.580  -8.804   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       0.790  -7.482   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -0.750  -7.505   0.000  0.00  0.00           C+0
HETATM   24  O   UNK     0      -1.499  -8.850   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      -3.039  -8.874   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   23                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7   22                                                  
CONECT    7    6    8                                                       
CONECT    8    7    9   20                                                  
CONECT    9    8   10   17                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   15                                                  
CONECT   12   11   13   16                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   11                                                       
CONECT   16   12   17                                                       
CONECT   17   16    9   18                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19    8   21                                                  
CONECT   21   20   22                                                       
CONECT   22   21    6   23                                                  
CONECT   23   22    3   24                                                  
CONECT   24   23   25                                                       
CONECT   25   24                                                            
MASTER        0    0    0    0    0    0    0    0   25    0   58    0
END

COMPND    HMDB0003409
HETATM    1  C1  UNL     1      -5.021   4.073  -0.218  1.00  0.00           C  
HETATM    2  O1  UNL     1      -4.612   2.806  -0.694  1.00  0.00           O  
HETATM    3  C2  UNL     1      -3.335   2.352  -0.410  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.465   3.126   0.332  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.188   2.663   0.611  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.788   1.430   0.148  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.488   0.915   0.402  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.878  -0.320  -0.065  1.00  0.00           C  
HETATM    9  N1  UNL     1       0.054  -1.090  -0.790  1.00  0.00           N1+
HETATM   10  C8  UNL     1      -1.199  -0.586  -1.038  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.629   0.633  -0.593  1.00  0.00           C  
HETATM   12  C10 UNL     1      -2.896   1.125  -0.854  1.00  0.00           C  
HETATM   13  O2  UNL     1      -3.741   0.333  -1.595  1.00  0.00           O  
HETATM   14  C11 UNL     1      -4.575  -0.582  -0.930  1.00  0.00           C  
HETATM   15  C12 UNL     1       0.377  -2.356  -1.380  1.00  0.00           C  
HETATM   16  C13 UNL     1       1.539  -3.051  -0.806  1.00  0.00           C  
HETATM   17  C14 UNL     1       2.509  -2.164  -0.164  1.00  0.00           C  
HETATM   18  C15 UNL     1       3.809  -2.607   0.115  1.00  0.00           C  
HETATM   19  C16 UNL     1       4.728  -1.827   0.779  1.00  0.00           C  
HETATM   20  C17 UNL     1       4.390  -0.561   1.197  1.00  0.00           C  
HETATM   21  C18 UNL     1       3.106  -0.108   0.927  1.00  0.00           C  
HETATM   22  C19 UNL     1       2.178  -0.902   0.252  1.00  0.00           C  
HETATM   23  O3  UNL     1       5.472   0.007   1.831  1.00  0.00           O  
HETATM   24  C20 UNL     1       6.276  -1.103   2.248  1.00  0.00           C  
HETATM   25  O4  UNL     1       6.056  -2.006   1.180  1.00  0.00           O  
HETATM   26  H1  UNL     1      -4.842   4.155   0.871  1.00  0.00           H  
HETATM   27  H2  UNL     1      -4.453   4.888  -0.741  1.00  0.00           H  
HETATM   28  H3  UNL     1      -6.109   4.209  -0.387  1.00  0.00           H  
HETATM   29  H4  UNL     1      -2.791   4.104   0.695  1.00  0.00           H  
HETATM   30  H5  UNL     1      -0.531   3.288   1.191  1.00  0.00           H  
HETATM   31  H6  UNL     1       1.114   1.562   0.985  1.00  0.00           H  
HETATM   32  H7  UNL     1      -1.895  -1.177  -1.617  1.00  0.00           H  
HETATM   33  H8  UNL     1      -5.274  -1.032  -1.666  1.00  0.00           H  
HETATM   34  H9  UNL     1      -5.200  -0.126  -0.143  1.00  0.00           H  
HETATM   35  H10 UNL     1      -3.984  -1.379  -0.452  1.00  0.00           H  
HETATM   36  H11 UNL     1       0.592  -2.181  -2.486  1.00  0.00           H  
HETATM   37  H12 UNL     1      -0.546  -3.031  -1.392  1.00  0.00           H  
HETATM   38  H13 UNL     1       1.226  -3.889  -0.108  1.00  0.00           H  
HETATM   39  H14 UNL     1       2.048  -3.607  -1.667  1.00  0.00           H  
HETATM   40  H15 UNL     1       4.059  -3.586  -0.213  1.00  0.00           H  
HETATM   41  H16 UNL     1       2.829   0.866   1.242  1.00  0.00           H  
HETATM   42  H17 UNL     1       7.356  -0.803   2.179  1.00  0.00           H  
HETATM   43  H18 UNL     1       5.991  -1.489   3.225  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3
CONECT    3    4    4   12
CONECT    4    5   29
CONECT    5    6    6   30
CONECT    6    7   11
CONECT    7    8    8   31
CONECT    8    9   22
CONECT    9   10   10   15
CONECT   10   11   32
CONECT   11   12   12
CONECT   12   13
CONECT   13   14
CONECT   14   33   34   35
CONECT   15   16   36   37
CONECT   16   17   38   39
CONECT   17   18   18   22
CONECT   18   19   40
CONECT   19   20   20   25
CONECT   20   21   23
CONECT   21   22   22   41
CONECT   23   24
CONECT   24   25   42   43
END

HMDB0003409
     RDKit          3D
Berberine
 43 47  0  0  0  0  0  0  0  0999 V2000
   -5.0207    4.0731   -0.2181 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6121    2.8063   -0.6944 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3354    2.3522   -0.4104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4647    3.1265    0.3315 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1881    2.6629    0.6107 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7876    1.4296    0.1481 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4881    0.9148    0.4024 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8776   -0.3205   -0.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0538   -1.0903   -0.7898 N   0  0  0  0  0  4  0  0  0  0  0  0
   -1.1993   -0.5861   -1.0384 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6290    0.6334   -0.5932 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8963    1.1249   -0.8544 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7407    0.3329   -1.5947 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5751   -0.5824   -0.9298 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3768   -2.3557   -1.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5389   -3.0508   -0.8057 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5089   -2.1636   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8089   -2.6067    0.1148 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7283   -1.8266    0.7788 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3901   -0.5608    1.1975 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1058   -0.1076    0.9271 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1780   -0.9022    0.2525 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722    0.0075    1.8313 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2755   -1.1031    2.2479 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0560   -2.0060    1.1800 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8422    4.1550    0.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4527    4.8882   -0.7406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1093    4.2086   -0.3867 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7907    4.1043    0.6949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5307    3.2883    1.1914 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1143    1.5623    0.9846 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8946   -1.1768   -1.6175 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2736   -1.0315   -1.6659 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2002   -0.1262   -0.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9839   -1.3788   -0.4525 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5919   -2.1808   -2.4864 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5461   -3.0311   -1.3915 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2260   -3.8887   -0.1077 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0476   -3.6075   -1.6673 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0585   -3.5855   -0.2132 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8289    0.8658    1.2418 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3562   -0.8030    2.1789 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.9908   -1.4895    3.2246 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  6  7  1  0
  7  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  1  0
  9 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 20 23  1  0
 23 24  1  0
 24 25  1  0
 12  3  1  0
 22 17  1  0
 11  6  1  0
 25 19  1  0
 22  8  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  4 29  1  0
  5 30  1  0
  7 31  1  0
 10 32  1  0
 14 33  1  0
 14 34  1  0
 14 35  1  0
 15 36  1  0
 15 37  1  0
 16 38  1  0
 16 39  1  0
 18 40  1  0
 21 41  1  0
 24 42  1  0
 24 43  1  0
M  CHG  1   9   1
M  END

View in JSmol

Synonyms

Value	Source
5,6-Dihydro-9,10-dimethoxy-1,3-benzodioxolo[5,6-a]benzo[g]quinolizinium	ChEBI
7,8,13,13a-Tetradehydro-9,10-dimethoxy-2,3-[methylenebis(oxy)]berbinium	ChEBI
9,10-Dimethoxy-2,3-(methylenedioxy)-7,8,13,13a-tetradehydroberbinium	ChEBI
Berberin	ChEBI
Coptis rhizome	HMDB

Chemical Formula

C₂₀H₁₈NO₄

Average Mass

336.3612 Da

Monoisotopic Mass

336.12358 Da

IUPAC Name

16,17-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 Name

16,17-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 Number

2086-83-1

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 Key

YBHILYKTIRIUTE-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, simulated)	V.dorna83			2021-09-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	V.dorna83			2021-09-06	View Spectrum
2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Not Available

Chemical Shift Submissions

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, simulated)	V.dorna83			2021-08-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, simulated)	V.dorna83			2021-07-20	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Achyranthes japonica	LOTUS Database	35616633
Anamirta cocculus	LOTUS Database	35616633
Andira inermis	LOTUS Database	35616633
Apis cerana	LOTUS Database	35616633
Arcangelisia flava	LOTUS Database	35616633
Archangelicia flava	-	KNApSAcK
Archangelisia spp.	-	KNApSAcK
Argemone mexicana	KNApSAcK Database	22123792
Argemone ochroleuca	LOTUS Database	35616633
Argemone platyceras	LOTUS Database	35616633
Argemone spp.	KNApSAcK Database	22123792
Argemone subfusiformia	KNApSAcK Database	22123792
Argemone subfusiformis	LOTUS Database	35616633
Argemone subfusiformis var.subinermis	KNApSAcK Database	22123792
Asteropyrum cavaleriei	KNApSAcK Database	22123792
Berberis aemulans	KNApSAcK Database	22123792
Berberis aggregata	LOTUS Database	35616633
Berberis amurensis	LOTUS Database	35616633
Berberis aquifolium	KNApSAcK Database	22123792
Berberis aristata	KNApSAcK Database	22123792
Berberis brandisiana	KNApSAcK Database	22123792
Berberis candidula	KNApSAcK Database	22123792
Berberis chitria	LOTUS Database	35616633
Berberis crataegina	LOTUS Database	35616633
Berberis cretica	LOTUS Database	35616633
Berberis croatica	KNApSAcK Database	22123792
Berberis darwinii	KNApSAcK Database	22123792
Berberis densiflora	KNApSAcK Database	22123792
Berberis diaphana	KNApSAcK Database	22123792
Berberis dubia	KNApSAcK Database	22123792
Berberis duclouxiana	LOTUS Database	35616633
Berberis empetrifolia	LOTUS Database	35616633
Berberis fendleri	LOTUS Database	35616633
Berberis gagnepainii	LOTUS Database	35616633
Berberis heterobotrys	KNApSAcK Database	22123792
Berberis heteropoda	LOTUS Database	35616633
Berberis ilicifolia	LOTUS Database	35616633
Berberis iliensis	KNApSAcK Database	22123792
Berberis integerrima	KNApSAcK Database	22123792
Berberis japonica	LOTUS Database	35616633
Berberis julianae	KNApSAcK Database	22123792
Berberis laurina	LOTUS Database	35616633
Berberis lycium	LOTUS Database	35616633
Berberis microphylla	LOTUS Database	35616633
Berberis nervosa	KNApSAcK Database	22123792
Berberis nummularia	LOTUS Database	35616633
Berberis numularis	KNApSAcK Database	22123792
Berberis oblonga	KNApSAcK Database	22123792
Berberis poirettii	KNApSAcK Database	22123792
Berberis potaninii	KNApSAcK Database	22123792
Berberis pruinosa	KNApSAcK Database	22123792
Berberis pseudanubalata	KNApSAcK Database	22123792
Berberis rigidifolia	KNApSAcK Database	22123792
Berberis sibirica	LOTUS Database	35616633
Berberis spp.	KNApSAcK Database	22123792
Berberis stenophylla	KNApSAcK Database	22123792
Berberis stolonifera	LOTUS Database	35616633
Berberis thunbergii	KNApSAcK Database	22123792
Berberis turcomanica	KNApSAcK Database	22123792
Berberis vulgaris	KNApSAcK Database	22123792
Berberis wilsonae	KNApSAcK Database	22123792
Berberis wilsoniae	KNApSAcK Database	22123792
Chelidonium majus	Plant	KNApSAcK
Chelidonium majus L.	KNApSAcK Database	22123792
Chelidonium spp.	KNApSAcK Database	22123792
Chelidonum majus	-	KNApSAcK
Cineraria deltoidea	Plant	KNApSAcK
Coptis chinensis	KNApSAcK Database	22123792
Coptis deltoidea	KNApSAcK Database	22123792
Coptis deltoides	KNApSAcK Database	22123792
Coptis gulinensis	KNApSAcK Database	22123792
Coptis japonica	KNApSAcK Database	22123792
Coptis linearisepala	KNApSAcK Database	22123792
Coptis omeiensis	KNApSAcK Database	22123792
Coptis quinquefolia	LOTUS Database	35616633
Coptis spp.	KNApSAcK Database	22123792
Coptis teeta	Plant	KNApSAcK
Coptis teetoides	KNApSAcK Database	22123792
Corydalis amunca	KNApSAcK Database	22123792
Corydalis intermedia	KNApSAcK Database	22123792
Corydalis ledebouriana	KNApSAcK Database	22123792
Corydalis longicalcarata	KNApSAcK Database	22123792
Corydalis ophiocarpa	KNApSAcK Database	22123792
Corydalis pallida	LOTUS Database	35616633
Corydalis remota	KNApSAcK Database	22123792
Corydalis solida	KNApSAcK Database	22123792
Corydalis speciosa	LOTUS Database	35616633
Corydalis spp.	KNApSAcK Database	22123792
Corydalis turtschaninovii	LOTUS Database	35616633
Corydalis yanhusuo	KNApSAcK Database	22123792
Coscinium fenestratum	KNApSAcK Database	22123792
Echinacea purpurea	LOTUS Database	35616633
Eschscholtzia california	KNApSAcK Database	22123792
Eschscholzia californica	LOTUS Database	35616633
Eschscholzia lobbii	LOTUS Database	35616633
Evodia mellifolia	KNApSAcK Database	22123792
Evodia spp.	KNApSAcK Database	22123792
Festuca ovina	LOTUS Database	35616633
Fibraurea chloroleuca	LOTUS Database	35616633
Glaucium arabicum	KNApSAcK Database	22123792
Glaucium squamigerum	LOTUS Database	35616633
Hydrastis canadensis	KNApSAcK Database	22123792
Macleaya cordata	KNApSAcK Database	22123792
Magnolia biondii	KNApSAcK Database	22123792
Mahania shenii	-	KNApSAcK
Mahonia aquifolium	KNApSAcK Database	22123792
Mahonia bealei	KNApSAcK Database	22123792
Mahonia bodinieri	KNApSAcK Database	22123792
Mahonia confusa	KNApSAcK Database	22123792
Mahonia eurybracteata	KNApSAcK Database	22123792
Mahonia fortunei	KNApSAcK Database	22123792
Mahonia gracilipes	KNApSAcK Database	22123792
Mahonia japonica	KNApSAcK Database	22123792
Mahonia repens	LOTUS Database	35616633
Mahonia spp.	KNApSAcK Database	22123792
Mahonia veitchiorum	KNApSAcK Database	22123792
Meconopsis cambrica	LOTUS Database	35616633
Mohonia bealei	-	KNApSAcK
Nandina domestica	KNApSAcK Database	22123792
Nandina spp.	KNApSAcK Database	22123792
Naravelia zeylandica	KNApSAcK Database	22123792
Papaver albiflora	KNApSAcK Database	22123792
Papaver bracteatum	KNApSAcK Database	22123792
Papaver confine	KNApSAcK Database	22123792
Papaver dubium	LOTUS Database	35616633
Papaver lapponicum	LOTUS Database	35616633
Papaver pinnatifidum	KNApSAcK Database	22123792
Papaver radicatum	KNApSAcK Database	22123792
Papaver rhoeas	LOTUS Database	35616633
Papaver rhoeas chelidonides	KNApSAcK Database	22123792
Papaver rhopalothece	KNApSAcK Database	22123792
Papaver somniferum	KNApSAcK Database	22123792
Papver stevenianum	-	KNApSAcK
Parabaena sagittata	LOTUS Database	35616633
Pausinylstalia yohimbe	-	KNApSAcK
Penianthus zenkeri	LOTUS Database	35616633
Phellodendron amurense	KNApSAcK Database	22123792
Phellodendron chinense	KNApSAcK Database	22123792
Phellodendron chinensis	KNApSAcK Database	22123792
Phellodendron lavallei	KNApSAcK Database	22123792
Phellodendron wilsonii	KNApSAcK Database	22123792
Ranunculus serbicus	KNApSAcK Database	22123792
Rollinia mucosa	LOTUS Database	35616633
Sanguinaria canadensis	LOTUS Database	35616633
Stephania cephalantha	Plant	KNApSAcK
Stephania cepharantha	KNApSAcK Database	22123792
Stephania tetrandra	KNApSAcK Database	22123792
Stylophorum diphyllum	LOTUS Database	35616633
Stylophorum lasiocarpum	KNApSAcK Database	22123792
Thalictrum atriplex	KNApSAcK Database	22123792
Thalictrum baicalense	LOTUS Database	35616633
Thalictrum cultratum	LOTUS Database	35616633
Thalictrum delavayi	LOTUS Database	35616633
Thalictrum dioicum	LOTUS Database	35616633
Thalictrum faberi	KNApSAcK Database	22123792
Thalictrum flavum	KNApSAcK Database	22123792
Thalictrum foetidum	KNApSAcK Database	22123792
Thalictrum foliolosum	KNApSAcK Database	22123792
Thalictrum foliosum	KNApSAcK Database	22123792
Thalictrum glandulosissimum	KNApSAcK Database	22123792
Thalictrum hernandezii	LOTUS Database	35616633
Thalictrum honanense	KNApSAcK Database	22123792
Thalictrum javanicum Blume	LOTUS Database	35616633
Thalictrum lankesteri	LOTUS Database	35616633
Thalictrum longipedunculatum	KNApSAcK Database	22123792
Thalictrum lucidum	LOTUS Database	35616633
Thalictrum microgynum	KNApSAcK Database	22123792
Thalictrum minus	KNApSAcK Database	22123792
Thalictrum minus var. hypoleucum	Plant	KNApSAcK
Thalictrum orientale	KNApSAcK Database	22123792
Thalictrum petaloideum	LOTUS Database	35616633
Thalictrum petaloidum	KNApSAcK Database	22123792
Thalictrum podocarpum	LOTUS Database	35616633
Thalictrum przewalskii	KNApSAcK Database	22123792
Thalictrum purpurescens	KNApSAcK Database	22123792
Thalictrum revolutum	LOTUS Database	35616633
Thalictrum simplex	KNApSAcK Database	22123792
Thalictrum spp.	KNApSAcK Database	22123792
Thalictrum symplex	KNApSAcK Database	22123792
Thalictrum thunbergii	KNApSAcK Database	22123792
Thalictrum tuberosum	LOTUS Database	35616633
Thalictrum wanqii	KNApSAcK Database	22123792
Tinospora cordifolia	LOTUS Database	35616633
Toddalia aculeata Pers.	KNApSAcK Database	22123792
Toddalia spp.	KNApSAcK Database	22123792
Xanthorhiza simplicissima	KNApSAcK Database	22123792
Zanthoxylum monophyllum	LOTUS Database	35616633
Zanthoxylum spp.	KNApSAcK Database	22123792
Ziziphus jujuba	KNApSAcK Database	22123792

Species Where Detected

Species Name	Source	Reference
Acangelisia gusanlung	KNApSAcK Database	22123792

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.

Kingdom

Organic compounds

Super Class

Alkaloids and derivatives

Class

Protoberberine alkaloids and derivatives

Sub Class

Not Available

Direct Parent

Protoberberine 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 Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heteropentacyclic compound (CHEBI:16118 )
berberine alkaloid (CHEBI:16118 )
alkaloid antibiotic (CHEBI:16118 )
botanical anti-fungal agent (CHEBI:16118 )
Alkaloids (C00757 )
Isoquinoline alkaloids (C00757 )
a small molecule (BERBERINE )

Physical Properties

State

Solid

Experimental Properties

Property	Value	Reference
Melting Point	145 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	9.62 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	-0.990 (est)	The Good Scents Company Information System

Predicted Properties

Property	Value	Source
Water Solubility	0.00035 g/L	ALOGPS
logP	-0.18	ALOGPS
logP	-1.3	ChemAxon
logS	-6	ALOGPS
pKa (Strongest Basic)	-4.4	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	40.8 Å²	ChemAxon
Rotatable Bond Count	2	ChemAxon
Refractivity	93.52 m³·mol⁻¹	ChemAxon
Polarizability	36.92 Å³	ChemAxon
Number of Rings	5	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

HMDB0003409

DrugBank ID

DB04115

Phenol Explorer Compound ID

Not Available

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Berberine

METLIN ID

3471

PubChem Compound

2353

PDB ID

Not Available

ChEBI ID

16118

Good Scents ID

rw1070241

References

General References

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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
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 ]
Song D, Hao J, Fan D: Biological properties and clinical applications of berberine. Front Med. 2020 Oct;14(5):564-582. doi: 10.1007/s11684-019-0724-6. Epub 2020 Apr 25. [PubMed:32335802 ]
Yin J, Xing H, Ye J: Efficacy of berberine in patients with type 2 diabetes mellitus. Metabolism. 2008 May;57(5):712-7. doi: 10.1016/j.metabol.2008.01.013. [PubMed:18442638 ]

Showing NP-Card for Berberine (NP0000008)

MOL for NP0000008 (Berberine)

3D MOL for NP0000008 (Berberine)

3D SDF for NP0000008 (Berberine)

3D-SDF for NP0000008 (Berberine)

PDB for NP0000008 (Berberine)

3D PDB for NP0000008 (Berberine)

SMILES for NP0000008 (Berberine)

INCHI for NP0000008 (Berberine)

Structure for NP0000008 (Berberine)

3D Structure for NP0000008 (Berberine)