Jump To Section:

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

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:35:48 UTC

Update Date

2022-03-07 02:52:29 UTC

HMDB ID

HMDB0030266

Secondary Accession Numbers

HMDB30266

Metabolite Identification

Common Name

Berberrubine

Description

Berberrubine, also known as 6847-93-4 or 9-berberoline, 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. Based on a literature review a significant number of articles have been published on Berberrubine.

Structure

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

HMDB0030266
     RDKit          3D
Berberrubine
 40 44  0  0  0  0  0  0  0  0999 V2000
    6.5262    1.6911    0.1858 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7257    0.5492    0.1683 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3336    0.6559    0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6902    1.8701    0.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3187    1.9723    0.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585    0.8233    0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.8863   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5604   -0.2838   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0204   -1.4908   -0.0106 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.3951   -1.5592    0.0375 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1572   -0.4164    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5520   -0.4914    0.1025 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2139   -1.6965    0.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7036   -2.7180   -0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1694   -2.6630   -0.0733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7540   -1.3242   -0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1379   -1.2621   -0.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7900   -0.0483   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0630    1.1199   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6657    1.0690   -0.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0302   -0.1478   -0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    2.1919   -0.2144 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2501    1.6945   -0.4268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1350    0.2923   -0.2377 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6350    2.1422   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0875    2.4166    0.9010 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5331    1.4283    0.5814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2493    2.7867    0.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8216    2.9280    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2820    1.8543   -0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8564   -2.5323    0.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8565   -2.6128    0.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3821   -3.3193    0.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2894   -3.3391   -0.8810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6202   -3.2346   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6152   -3.1691    0.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7365   -2.1609   -0.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1312    1.9970   -0.1160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5440    1.9215   -1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9111    2.1791    0.2969 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
  9 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 19 22  1  0
 22 23  1  0
 23 24  1  0
 12  3  1  0
 21 16  1  0
 11  6  1  0
 24 18  1  0
 21  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  7 30  1  0
 10 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  0
 15 36  1  0
 17 37  1  0
 20 38  1  0
 23 39  1  0
 23 40  1  0
M  CHG  1   9   1
M  END


  Mrv1652305171805372D          

 24 28  0  0  0  0            999 V2000
    1.9804   -1.6597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9804   -0.0126    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6908   -0.4212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6908   -1.2511    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1242   -0.4150    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4012    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1242   -1.2448    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
    3.4075   -1.6597    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4138   -2.4833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8409   -1.6472    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8472   -2.4833    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1305   -2.8983    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1367   -3.7218    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8534   -4.1305    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5639   -3.7093    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5576   -2.8857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2699   -1.2448    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2637   -0.4212    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4841   -0.1697    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8424    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4904   -1.5026    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2680   -2.4707    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2806   -4.1179    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2869   -4.9352    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1 17  1  0  0  0  0
  1  4  2  0  0  0  0
  2  3  2  0  0  0  0
  2 18  1  0  0  0  0
  3  6  1  0  0  0  0
  3  4  1  0  0  0  0
  4  8  1  0  0  0  0
  5  7  1  0  0  0  0
  5  6  1  0  0  0  0
  7  8  1  0  0  0  0
  7 10  2  0  0  0  0
  8  9  2  0  0  0  0
  9 12  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 16  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 23  1  0  0  0  0
 16 22  1  0  0  0  0
 17 18  2  0  0  0  0
 17 21  1  0  0  0  0
 18 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 23 24  1  0  0  0  0
M  CHG  1   7   1
M  END
> <DATABASE_ID>
HMDB0030266

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2

> <INCHI_IDENTIFIER>
InChI=1S/C19H15NO4/c1-22-16-3-2-11-6-15-13-8-18-17(23-10-24-18)7-12(13)4-5-20(15)9-14(11)19(16)21/h2-3,6-9H,4-5,10H2,1H3/p+1

> <INCHI_KEY>
GLYPKDKODVRYGP-UHFFFAOYSA-O

> <FORMULA>
C19H16NO4

> <MOLECULAR_WEIGHT>
322.3346

> <EXACT_MASS>
322.107933005

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
40

> <JCHEM_AVERAGE_POLARIZABILITY>
34.89521097604788

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
1

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
16-hydroxy-17-methoxy-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(20),16,18-octaen-13-ylium

> <ALOGPS_LOGP>
-0.31

> <JCHEM_LOGP>
-1.4292063418050789

> <ALOGPS_LOGS>
-5.34

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
5

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.271586535140377

> <JCHEM_PKA_STRONGEST_BASIC>
-4.519862373583301

> <JCHEM_POLAR_SURFACE_AREA>
51.8

> <JCHEM_REFRACTIVITY>
89.04100000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.63e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
16-hydroxy-17-methoxy-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(20),16,18-octaen-13-ylium

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0030266
     RDKit          3D
Berberrubine
 40 44  0  0  0  0  0  0  0  0999 V2000
    6.5262    1.6911    0.1858 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7257    0.5492    0.1683 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3336    0.6559    0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6902    1.8701    0.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3187    1.9723    0.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585    0.8233    0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.8863   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5604   -0.2838   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0204   -1.4908   -0.0106 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.3951   -1.5592    0.0375 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1572   -0.4164    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5520   -0.4914    0.1025 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2139   -1.6965    0.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7036   -2.7180   -0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1694   -2.6630   -0.0733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7540   -1.3242   -0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1379   -1.2621   -0.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7900   -0.0483   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0630    1.1199   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6657    1.0690   -0.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0302   -0.1478   -0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    2.1919   -0.2144 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2501    1.6945   -0.4268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1350    0.2923   -0.2377 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6350    2.1422   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0875    2.4166    0.9010 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5331    1.4283    0.5814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2493    2.7867    0.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8216    2.9280    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2820    1.8543   -0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8564   -2.5323    0.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8565   -2.6128    0.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3821   -3.3193    0.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2894   -3.3391   -0.8810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6202   -3.2346   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6152   -3.1691    0.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7365   -2.1609   -0.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1312    1.9970   -0.1160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5440    1.9215   -1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9111    2.1791    0.2969 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
  9 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 19 22  1  0
 22 23  1  0
 23 24  1  0
 12  3  1  0
 21 16  1  0
 11  6  1  0
 24 18  1  0
 21  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  7 30  1  0
 10 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  0
 15 36  1  0
 17 37  1  0
 20 38  1  0
 23 39  1  0
 23 40  1  0
M  CHG  1   9   1
M  END

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       3.697  -3.098   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.697  -0.023   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.023  -0.786   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.023  -2.335   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.698  -0.775   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.349   0.000   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0       7.698  -2.324   0.000  0.00  0.00           N+1
HETATM    8  C   UNK     0       6.361  -3.098   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       6.372  -4.635   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       9.036  -3.075   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       9.048  -4.635   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       7.710  -5.410   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       7.722  -6.947   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       9.060  -7.710   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.386  -6.924   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.374  -5.387   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       2.371  -2.324   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       2.359  -0.786   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0       0.904  -0.317   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0       0.000  -1.573   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0       0.915  -2.805   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      11.700  -4.612   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      11.724  -7.687   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      11.736  -9.212   0.000  0.00  0.00           C+0
CONECT    1   17    4                                                       
CONECT    2    3   18                                                       
CONECT    3    2    6    4                                                  
CONECT    4    1    3    8                                                  
CONECT    5    7    6                                                       
CONECT    6    3    5                                                       
CONECT    7    5    8   10                                                  
CONECT    8    4    7    9                                                  
CONECT    9    8   12                                                       
CONECT   10    7   11                                                       
CONECT   11   10   12   16                                                  
CONECT   12    9   11   13                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   23                                                  
CONECT   16   11   15   22                                                  
CONECT   17    1   18   21                                                  
CONECT   18    2   17   19                                                  
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   17   20                                                       
CONECT   22   16                                                            
CONECT   23   15   24                                                       
CONECT   24   23                                                            
MASTER        0    0    0    0    0    0    0    0   24    0   56    0
END

COMPND    HMDB0030266
HETATM    1  C1  UNL     1       6.526   1.691   0.186  1.00  0.00           C  
HETATM    2  O1  UNL     1       5.726   0.549   0.168  1.00  0.00           O  
HETATM    3  C2  UNL     1       4.334   0.656   0.119  1.00  0.00           C  
HETATM    4  C3  UNL     1       3.690   1.870   0.086  1.00  0.00           C  
HETATM    5  C4  UNL     1       2.319   1.972   0.038  1.00  0.00           C  
HETATM    6  C5  UNL     1       1.558   0.823   0.022  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.181   0.886  -0.026  1.00  0.00           C  
HETATM    8  C7  UNL     1      -0.560  -0.284  -0.041  1.00  0.00           C  
HETATM    9  N1  UNL     1       0.020  -1.491  -0.011  1.00  0.00           N1+
HETATM   10  C8  UNL     1       1.395  -1.559   0.037  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.157  -0.416   0.054  1.00  0.00           C  
HETATM   12  C10 UNL     1       3.552  -0.491   0.102  1.00  0.00           C  
HETATM   13  O2  UNL     1       4.214  -1.697   0.136  1.00  0.00           O  
HETATM   14  C11 UNL     1      -0.704  -2.718  -0.025  1.00  0.00           C  
HETATM   15  C12 UNL     1      -2.169  -2.663  -0.073  1.00  0.00           C  
HETATM   16  C13 UNL     1      -2.754  -1.324  -0.106  1.00  0.00           C  
HETATM   17  C14 UNL     1      -4.138  -1.262  -0.155  1.00  0.00           C  
HETATM   18  C15 UNL     1      -4.790  -0.048  -0.188  1.00  0.00           C  
HETATM   19  C16 UNL     1      -4.063   1.120  -0.174  1.00  0.00           C  
HETATM   20  C17 UNL     1      -2.666   1.069  -0.126  1.00  0.00           C  
HETATM   21  C18 UNL     1      -2.030  -0.148  -0.093  1.00  0.00           C  
HETATM   22  O3  UNL     1      -4.941   2.192  -0.214  1.00  0.00           O  
HETATM   23  C19 UNL     1      -6.250   1.695  -0.427  1.00  0.00           C  
HETATM   24  O4  UNL     1      -6.135   0.292  -0.238  1.00  0.00           O  
HETATM   25  H1  UNL     1       6.635   2.142  -0.822  1.00  0.00           H  
HETATM   26  H2  UNL     1       6.088   2.417   0.901  1.00  0.00           H  
HETATM   27  H3  UNL     1       7.533   1.428   0.581  1.00  0.00           H  
HETATM   28  H4  UNL     1       4.249   2.787   0.098  1.00  0.00           H  
HETATM   29  H5  UNL     1       1.822   2.928   0.013  1.00  0.00           H  
HETATM   30  H6  UNL     1      -0.282   1.854  -0.051  1.00  0.00           H  
HETATM   31  H7  UNL     1       1.856  -2.532   0.062  1.00  0.00           H  
HETATM   32  H8  UNL     1       3.857  -2.613   0.132  1.00  0.00           H  
HETATM   33  H9  UNL     1      -0.382  -3.319   0.876  1.00  0.00           H  
HETATM   34  H10 UNL     1      -0.289  -3.339  -0.881  1.00  0.00           H  
HETATM   35  H11 UNL     1      -2.620  -3.235  -0.923  1.00  0.00           H  
HETATM   36  H12 UNL     1      -2.615  -3.169   0.836  1.00  0.00           H  
HETATM   37  H13 UNL     1      -4.737  -2.161  -0.167  1.00  0.00           H  
HETATM   38  H14 UNL     1      -2.131   1.997  -0.116  1.00  0.00           H  
HETATM   39  H15 UNL     1      -6.544   1.922  -1.475  1.00  0.00           H  
HETATM   40  H16 UNL     1      -6.911   2.179   0.297  1.00  0.00           H  
CONECT    1    2   25   26   27
CONECT    2    3
CONECT    3    4    4   12
CONECT    4    5   28
CONECT    5    6    6   29
CONECT    6    7   11
CONECT    7    8    8   30
CONECT    8    9   21
CONECT    9   10   10   14
CONECT   10   11   31
CONECT   11   12   12
CONECT   12   13
CONECT   13   32
CONECT   14   15   33   34
CONECT   15   16   35   36
CONECT   16   17   17   21
CONECT   17   18   37
CONECT   18   19   19   24
CONECT   19   20   22
CONECT   20   21   21   38
CONECT   22   23
CONECT   23   24   39   40
END

HMDB0030266
     RDKit          3D
Berberrubine
 40 44  0  0  0  0  0  0  0  0999 V2000
    6.5262    1.6911    0.1858 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7257    0.5492    0.1683 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3336    0.6559    0.1193 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6902    1.8701    0.0864 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3187    1.9723    0.0381 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5585    0.8233    0.0221 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1808    0.8863   -0.0260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5604   -0.2838   -0.0413 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0204   -1.4908   -0.0106 N   0  0  0  0  0  4  0  0  0  0  0  0
    1.3951   -1.5592    0.0375 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1572   -0.4164    0.0537 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5520   -0.4914    0.1025 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2139   -1.6965    0.1360 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7036   -2.7180   -0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1694   -2.6630   -0.0733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7540   -1.3242   -0.1064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1379   -1.2621   -0.1546 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7900   -0.0483   -0.1883 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0630    1.1199   -0.1742 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6657    1.0690   -0.1257 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0302   -0.1478   -0.0925 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9408    2.1919   -0.2144 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2501    1.6945   -0.4268 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1350    0.2923   -0.2377 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.6350    2.1422   -0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0875    2.4166    0.9010 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5331    1.4283    0.5814 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2493    2.7867    0.0976 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8216    2.9280    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2820    1.8543   -0.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8564   -2.5323    0.0620 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8565   -2.6128    0.1318 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3821   -3.3193    0.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2894   -3.3391   -0.8810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6202   -3.2346   -0.9235 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6152   -3.1691    0.8364 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7365   -2.1609   -0.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1312    1.9970   -0.1160 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5440    1.9215   -1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9111    2.1791    0.2969 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
  9 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 17 18  1  0
 18 19  2  0
 19 20  1  0
 20 21  2  0
 19 22  1  0
 22 23  1  0
 23 24  1  0
 12  3  1  0
 21 16  1  0
 11  6  1  0
 24 18  1  0
 21  8  1  0
  1 25  1  0
  1 26  1  0
  1 27  1  0
  4 28  1  0
  5 29  1  0
  7 30  1  0
 10 31  1  0
 13 32  1  0
 14 33  1  0
 14 34  1  0
 15 35  1  0
 15 36  1  0
 17 37  1  0
 20 38  1  0
 23 39  1  0
 23 40  1  0
M  CHG  1   9   1
M  END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
6847-93-4	HMDB
9-Berberoline	HMDB
9-Berberoline chloride	HMDB
Berberrubine chloride	HMDB
5,6-Dihydro-9-hydroxy-10-methoxybenzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium chloride	HMDB
Berberrubine	MeSH

Chemical Formula

C₁₉H₁₆NO₄

Average Molecular Weight

322.3346

Monoisotopic Molecular Weight

322.107933005

IUPAC Name

16-hydroxy-17-methoxy-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(20),16,18-octaen-13-ylium

Traditional Name

16-hydroxy-17-methoxy-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(20),16,18-octaen-13-ylium

CAS Registry Number

17388-19-1

SMILES

COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2

InChI Identifier

InChI=1S/C19H15NO4/c1-22-16-3-2-11-6-15-13-8-18-17(23-10-24-18)7-12(13)4-5-20(15)9-14(11)19(16)21/h2-3,6-9H,4-5,10H2,1H3/p+1

InChI Key

GLYPKDKODVRYGP-UHFFFAOYSA-O

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
1-hydroxy-4-unsubstituted benzenoid
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

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Extracellular (HMDB: HMDB0030266)
Cytoplasm (HMDB: HMDB0030266)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0030266)

Source

Endogenous

Endogenous (HMDB: HMDB0030266)

Plant

Plant (HMDB: HMDB0030266)

Exogenous

Food

Food (HMDB: HMDB0030266)

Tea

Fruit

Fruits (FooDB: FOOD00871)

Process

Not Available

Role

Not Available

Physical Properties

State

Not Available

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	21.06 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.0028 g/L	ALOGPS
logP	-0.31	ALOGPS
logP	-1.4	ChemAxon
logS	-5.3	ALOGPS
pKa (Strongest Acidic)	8.27	ChemAxon
pKa (Strongest Basic)	-4.5	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	51.8 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	89.04 m³·mol⁻¹	ChemAxon
Polarizability	34.9 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]+	179.404	30932474
DeepCCS	[M-H]-	177.046	30932474
DeepCCS	[M-2H]-	210.756	30932474
DeepCCS	[M+Na]+	185.983	30932474
AllCCS	[M+H]+	175.7	32859911
AllCCS	[M+H-H2O]+	172.4	32859911
AllCCS	[M+NH4]+	178.8	32859911
AllCCS	[M+Na]+	179.7	32859911
AllCCS	[M-H]-	183.0	32859911
AllCCS	[M+Na-2H]-	182.4	32859911
AllCCS	[M+HCOO]-	181.8	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Berberrubine	COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2	4419.3	Standard polar	33892256
Berberrubine	COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2	2843.7	Standard non polar	33892256
Berberrubine	COC1=C(O)C2=C(C=C1)C=C1C3=CC4=C(OCO4)C=C3CC[N+]1=C2	3367.3	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Berberrubine,1TMS,isomer #1	COC1=CC=C2C=C3C4=CC5=C(C=C4CC[N+]3=CC2=C1O[Si](C)(C)C)OCO5	3228.4	Semi standard non polar	33892256
Berberrubine,1TBDMS,isomer #1	COC1=CC=C2C=C3C4=CC5=C(C=C4CC[N+]3=CC2=C1O[Si](C)(C)C(C)(C)C)OCO5	3459.1	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 - Berberrubine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0fkc-0491000000-53e48c359255f28d48ca	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Berberrubine 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
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 10V, Positive-QTOF	splash10-00di-0009000000-40ec3e631f941c5a2713	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 20V, Positive-QTOF	splash10-00di-0009000000-76ad903faa56ec526394	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 40V, Positive-QTOF	splash10-0bt9-2293000000-e57d7291bbbcafda9e65	2016-06-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 10V, Negative-QTOF	splash10-00di-0009000000-dcf7ab775a1e5de918ad	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 20V, Negative-QTOF	splash10-00di-0009000000-e219118afc5ca46236ff	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 40V, Negative-QTOF	splash10-0ab9-6439000000-22e251b7c346e3e107c9	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 10V, Positive-QTOF	splash10-00di-0009000000-f52046137381c8e84ef0	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 20V, Positive-QTOF	splash10-00di-0029000000-b9911b2c91c369109433	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berberrubine 40V, Positive-QTOF	splash10-024i-0092000000-a51b2504a55540662d4a	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-30	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm
Extracellular

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB002095

KNApSAcK ID

C00026111

Chemspider ID

65548

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

72704

PDB ID

Not Available

ChEBI ID

441632

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1818521

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Park KD, Lee JH, Kim SH, Kang TH, Moon JS, Kim SU: Synthesis of 13-(substituted benzyl) berberine and berberrubine derivatives as antifungal agents. Bioorg Med Chem Lett. 2006 Aug 1;16(15):3913-6. Epub 2006 May 30. [PubMed:16730982 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Berberrubine (HMDB0030266)

MOL for HMDB0030266 (Berberrubine)

3D MOL for HMDB0030266 (Berberrubine)

3D SDF for HMDB0030266 (Berberrubine)

3D-SDF for HMDB0030266 (Berberrubine)

PDB for HMDB0030266 (Berberrubine)

3D PDB for HMDB0030266 (Berberrubine)

SMILES for HMDB0030266 (Berberrubine)

INCHI for HMDB0030266 (Berberrubine)

Structure for HMDB0030266 (Berberrubine)

3D Structure for HMDB0030266 (Berberrubine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra