Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References XML

Record Information

Version

5.0

Status

Detected and Quantified

Creation Date

2006-08-12 20:17:34 UTC

Update Date

2022-03-07 02:49:18 UTC

HMDB ID

HMDB0003409

Secondary Accession Numbers

HMDB03409

Metabolite 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>
HMDB0003409

> <DATABASE_NAME>
hmdb

> <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 View NMR Assignments View Stereo Labels

Synonyms

Value	Source
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 Molecular Weight

336.3612

Monoisotopic Molecular Weight

336.123583069

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

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 )

Ontology

Not Available

Physical Properties

State

Solid

Experimental Molecular 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

Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M+H]+	Not Available	175.882	http://allccs.zhulab.cn/database/detail?ID=AllCCS00001369

Predicted Molecular 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M+H]+	185.893	30932474
DeepCCS	[M-H]-	182.918	30932474
DeepCCS	[M-2H]-	218.274	30932474
DeepCCS	[M+Na]+	194.564	30932474
AllCCS	[M+H]+	179.4	32859911
AllCCS	[M+H-H2O]+	176.1	32859911
AllCCS	[M+NH4]+	182.4	32859911
AllCCS	[M+Na]+	183.2	32859911
AllCCS	[M-H]-	187.3	32859911
AllCCS	[M+Na-2H]-	186.8	32859911
AllCCS	[M+HCOO]-	186.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Berberine	COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC	4258.7	Standard polar	33892256
Berberine	COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC	2841.7	Standard non polar	33892256
Berberine	COC1=CC=C2C=C3C4=CC5=C(OCO5)C=C4CC[N+]3=CC2=C1OC	3266.6	Semi standard non polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Berberine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0a4l-0059000000-2d03f2d248021273bb66	2017-08-28	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Berberine GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine Quattro_QQQ 10V, Positive-QTOF (Annotated)	splash10-000i-0009000000-19928d40d547cbbc26dc	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine Quattro_QQQ 25V, Positive-QTOF (Annotated)	splash10-00di-0029000000-42f72c3da8025ad70c4d	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine Quattro_QQQ 40V, Positive-QTOF (Annotated)	splash10-0103-0089000000-dbcf680bd232ed620a00	2012-07-25	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 10V, Positive-QTOF	splash10-000i-0009000000-2993f75f22b9532dc39f	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 20V, Positive-QTOF	splash10-000i-0009000000-1d4cdb20920f8c900320	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 30V, Positive-QTOF	splash10-0079-0019000000-4995338b7526764bbad3	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 40V, Positive-QTOF	splash10-00dl-0059000000-ab35b8a7ec73f1063bb2	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ (API3000, Applied Biosystems) 50V, Positive-QTOF	splash10-00fu-0089000000-09273e18fcd3186156f0	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOF	splash10-00di-0039000000-3a3f7eba3883c388e58c	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOF	splash10-0006-0092000000-6f10979e1ecdd29611b1	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-IT (LC/MSD Trap XCT, Agilent Technologies) , Positive-QTOF	splash10-0006-0090000000-bacf940c54361560b64b	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-ITTOF (Shimadzu LC20A-IT-TOFMS) , Positive-QTOF	splash10-000i-0009000000-3d6d1928f5797f4633e4	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-ITTOF (LCMS-IT-TOF) , Positive-QTOF	splash10-000i-0009000000-6337ae6880e36d106adf	2012-08-31	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ , positive-QTOF	splash10-00dl-0039000000-5d1ff6b7636484db90d1	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QQ , positive-QTOF	splash10-00dl-0059000000-131055c16d28a84b6130	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOF	splash10-000i-0009000000-9d8986d4bd9f3b6d634d	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOF	splash10-000i-0009000000-4459c8c8f7b607ad7b49	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOF	splash10-00dr-0019000000-a0c1c55261d223b09256	2017-09-14	HMDB team, MONA	View Spectrum
Experimental LC-MS/MS	LC-MS/MS Spectrum - Berberine LC-ESI-QTOF , positive-QTOF	splash10-00dl-0069000000-437bdc5509b367efef25	2017-09-14	HMDB team, MONA	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 10V, Positive-QTOF	splash10-000i-0009000000-41bc0e7901cbc892051c	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 20V, Positive-QTOF	splash10-000i-0009000000-b2e1ddadd60e4f52d2dd	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 40V, Positive-QTOF	splash10-0iki-0179000000-85594d2e5f4b265077ab	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 10V, Negative-QTOF	splash10-000i-0009000000-604df9f348201c3c531e	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 20V, Negative-QTOF	splash10-000i-0009000000-34b3c7d90696ff194395	2017-07-26	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberine 40V, Negative-QTOF	splash10-0nnc-3095000000-2e76003cd5b376964ba8	2017-07-26	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-24	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 1D NMR	¹H NMR Spectrum (1D, 600 MHz, Methanol, experimental)	2021-10-10	Wishart Lab	View Spectrum
Experimental 2D NMR	[¹H, ¹³C]-HSQC NMR Spectrum (2D, 600 MHz, CD₃OD, experimental)	2012-12-05	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane (predicted from logP)

Biospecimen Locations

Blood

Tissue Locations

Fibroblasts
Intestine
Prostate

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected and Quantified	0.0013 +/- 0.0012 uM	Adult (>18 years old)	Both	Normal	17531424	details

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

DB04115

Phenol Explorer Compound ID

Not Available

FooDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Berberine

METLIN ID

3471

PubChem Compound

2353

PDB ID

Not Available

ChEBI ID

16118

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1070241

References

Synthesis Reference

Dominguez, 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

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 metabocard for Berberine (HMDB0003409)

MOL for HMDB0003409 (Berberine)

3D MOL for HMDB0003409 (Berberine)

3D SDF for HMDB0003409 (Berberine)

3D-SDF for HMDB0003409 (Berberine)

PDB for HMDB0003409 (Berberine)

3D PDB for HMDB0003409 (Berberine)

SMILES for HMDB0003409 (Berberine)

INCHI for HMDB0003409 (Berberine)

Structure for HMDB0003409 (Berberine)

3D Structure for HMDB0003409 (Berberine)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra