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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-11 03:34:16 UTC

Update Date

2021-09-26 22:59:42 UTC

HMDB ID

HMDB0249085

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Berbine

Description

berbine 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. berbine is a very strong basic compound (based on its pKa). This compound has been identified in human blood as reported by (PMID: 31557052 ). Berbine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Berbine is part of the human exposome. The exposome can be defined as the collection of all the exposures of an individual in a lifetime and how those exposures relate to health. An individual's exposure begins before birth and includes insults from environmental and occupational sources.

Structure

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

HMDB0249085
     RDKit          3D
Berbine
 35 38  0  0  0  0  0  0  0  0999 V2000
   -4.4007    1.1322   -0.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6977   -0.2032    0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6592   -1.1051    0.2591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3456   -0.7191    0.2888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0583    0.6240    0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0732    1.5556   -0.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6748    1.1492    0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3152    0.0856    0.6624 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6509    0.6031    0.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9355    1.9367    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2054    2.3840   -0.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1938    1.4308   -0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558    0.0893   -0.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649   -0.3122    0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3984   -1.7271    0.4145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0071   -2.1649    0.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0357   -1.1273    0.0032 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2510   -1.6718    0.4579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2089    1.8328   -0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7201   -0.5595    0.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9279   -2.1508    0.3623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8707    2.6081   -0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442    1.9643    0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3956    1.5194   -0.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2451    0.0532    1.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1301    2.6428    0.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4077    3.4530   -0.3779 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1865    1.7673   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7702   -0.6039   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6245   -1.9582    1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1378   -2.3144   -0.1699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6715   -2.8996    0.8712 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0169   -2.7117   -0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1875   -2.0379    1.5003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4379   -2.5648   -0.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  6  1  1  0
 17  8  1  0
 18  4  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  3 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
 16 33  1  0
 18 34  1  0
 18 35  1  0
M  END

  Mrv1533004241518482D          

 18 21  0  0  0  0            999 V2000
    1.2546    1.9716    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0647    2.1275    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6048    1.5039    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.4149    1.6598    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9550    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7651    1.1921    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3052    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0352   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6850    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8748    0.1007    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3347    0.7243    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5246    0.5684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2546   -0.2111    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4444   -0.3671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0957    0.2566    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1744    1.0361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9845    1.1921    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  1  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
  5 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
  3 12  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
 16 17  1  0  0  0  0
 17 18  2  0  0  0  0
 13 18  1  0  0  0  0
  1 18  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0249085

> <DATABASE_NAME>
hmdb

> <SMILES>
C1CC2=CC=CC=C2C2CC3=CC=CC=C3CN12

> <INCHI_IDENTIFIER>
InChI=1S/C17H17N/c1-2-7-15-12-18-10-9-13-5-3-4-8-16(13)17(18)11-14(15)6-1/h1-8,17H,9-12H2

> <INCHI_KEY>
BRLDZKPJJNASGG-UHFFFAOYSA-N

> <FORMULA>
C17H17N

> <MOLECULAR_WEIGHT>
235.33

> <EXACT_MASS>
235.136099551

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
35

> <JCHEM_AVERAGE_POLARIZABILITY>
27.833660753849735

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7,8,12b,13-tetrahydro-5H-6-azatetraphene

> <ALOGPS_LOGP>
3.54

> <JCHEM_LOGP>
3.7786597829999993

> <ALOGPS_LOGS>
-4.22

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA_STRONGEST_BASIC>
6.726011062412285

> <JCHEM_POLAR_SURFACE_AREA>
3.24

> <JCHEM_REFRACTIVITY>
75.50270000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.41e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
berbine

> <JCHEM_VEBER_RULE>
1

$$$$

HMDB0249085
     RDKit          3D
Berbine
 35 38  0  0  0  0  0  0  0  0999 V2000
   -4.4007    1.1322   -0.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6977   -0.2032    0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6592   -1.1051    0.2591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3456   -0.7191    0.2888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0583    0.6240    0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0732    1.5556   -0.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6748    1.1492    0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3152    0.0856    0.6624 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6509    0.6031    0.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9355    1.9367    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2054    2.3840   -0.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1938    1.4308   -0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558    0.0893   -0.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649   -0.3122    0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3984   -1.7271    0.4145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0071   -2.1649    0.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0357   -1.1273    0.0032 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2510   -1.6718    0.4579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2089    1.8328   -0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7201   -0.5595    0.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9279   -2.1508    0.3623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8707    2.6081   -0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442    1.9643    0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3956    1.5194   -0.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2451    0.0532    1.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1301    2.6428    0.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4077    3.4530   -0.3779 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1865    1.7673   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7702   -0.6039   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6245   -1.9582    1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1378   -2.3144   -0.1699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6715   -2.8996    0.8712 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0169   -2.7117   -0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1875   -2.0379    1.5003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4379   -2.5648   -0.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  6  1  1  0
 17  8  1  0
 18  4  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  3 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
 16 33  1  0
 18 34  1  0
 18 35  1  0
M  END

HEADER    PROTEIN                                 24-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-APR-15         0                                  
HETATM    1  C   UNK     0       2.342   3.680   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.854   3.971   0.000  0.00  0.00           C+0
HETATM    3  N   UNK     0       4.862   2.807   0.000  0.00  0.00           N+0
HETATM    4  C   UNK     0       6.375   3.098   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.383   1.934   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.895   2.225   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       9.903   1.061   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.399  -0.394   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.887  -0.685   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.879   0.479   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.366   0.188   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       4.358   1.352   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.846   1.061   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.342  -0.394   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       0.830  -0.685   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -0.179   0.479   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       0.326   1.934   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       1.838   2.225   0.000  0.00  0.00           C+0
CONECT    1    2   18                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4   12                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   10                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    5   11                                                  
CONECT   11   10   12                                                       
CONECT   12   11    3   13                                                  
CONECT   13   12   14   18                                                  
CONECT   14   13   15                                                       
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18                                                       
CONECT   18   17   13    1                                                  
MASTER        0    0    0    0    0    0    0    0   18    0   42    0
END

COMPND    HMDB0249085
HETATM    1  C1  UNL     1      -4.401   1.132  -0.035  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.698  -0.203   0.099  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.659  -1.105   0.259  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.346  -0.719   0.289  1.00  0.00           C  
HETATM    5  C5  UNL     1      -2.058   0.624   0.153  1.00  0.00           C  
HETATM    6  C6  UNL     1      -3.073   1.556  -0.009  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.675   1.149   0.170  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.315   0.086   0.662  1.00  0.00           C  
HETATM    9  C9  UNL     1       1.651   0.603   0.316  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.936   1.937   0.106  1.00  0.00           C  
HETATM   11  C11 UNL     1       3.205   2.384  -0.215  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.194   1.431  -0.320  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.956   0.089  -0.119  1.00  0.00           C  
HETATM   14  C14 UNL     1       2.665  -0.312   0.202  1.00  0.00           C  
HETATM   15  C15 UNL     1       2.398  -1.727   0.414  1.00  0.00           C  
HETATM   16  C16 UNL     1       1.007  -2.165   0.111  1.00  0.00           C  
HETATM   17  N1  UNL     1       0.036  -1.127   0.003  1.00  0.00           N  
HETATM   18  C17 UNL     1      -1.251  -1.672   0.458  1.00  0.00           C  
HETATM   19  H1  UNL     1      -5.209   1.833  -0.159  1.00  0.00           H  
HETATM   20  H2  UNL     1      -5.720  -0.560   0.082  1.00  0.00           H  
HETATM   21  H3  UNL     1      -3.928  -2.151   0.362  1.00  0.00           H  
HETATM   22  H4  UNL     1      -2.871   2.608  -0.117  1.00  0.00           H  
HETATM   23  H5  UNL     1      -0.644   1.964   0.943  1.00  0.00           H  
HETATM   24  H6  UNL     1      -0.396   1.519  -0.837  1.00  0.00           H  
HETATM   25  H7  UNL     1       0.245   0.053   1.765  1.00  0.00           H  
HETATM   26  H8  UNL     1       1.130   2.643   0.200  1.00  0.00           H  
HETATM   27  H9  UNL     1       3.408   3.453  -0.378  1.00  0.00           H  
HETATM   28  H10 UNL     1       5.187   1.767  -0.570  1.00  0.00           H  
HETATM   29  H11 UNL     1       4.770  -0.604  -0.216  1.00  0.00           H  
HETATM   30  H12 UNL     1       2.624  -1.958   1.490  1.00  0.00           H  
HETATM   31  H13 UNL     1       3.138  -2.314  -0.170  1.00  0.00           H  
HETATM   32  H14 UNL     1       0.672  -2.900   0.871  1.00  0.00           H  
HETATM   33  H15 UNL     1       1.017  -2.712  -0.857  1.00  0.00           H  
HETATM   34  H16 UNL     1      -1.187  -2.038   1.500  1.00  0.00           H  
HETATM   35  H17 UNL     1      -1.438  -2.565  -0.192  1.00  0.00           H  
CONECT    1    2    2    6   19
CONECT    2    3   20
CONECT    3    4    4   21
CONECT    4    5   18
CONECT    5    6    6    7
CONECT    6   22
CONECT    7    8   23   24
CONECT    8    9   17   25
CONECT    9   10   10   14
CONECT   10   11   26
CONECT   11   12   12   27
CONECT   12   13   28
CONECT   13   14   14   29
CONECT   14   15
CONECT   15   16   30   31
CONECT   16   17   32   33
CONECT   17   18
CONECT   18   34   35
END

HMDB0249085
     RDKit          3D
Berbine
 35 38  0  0  0  0  0  0  0  0999 V2000
   -4.4007    1.1322   -0.0351 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6977   -0.2032    0.0992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6592   -1.1051    0.2591 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3456   -0.7191    0.2888 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0583    0.6240    0.1531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0732    1.5556   -0.0089 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6748    1.1492    0.1703 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3152    0.0856    0.6624 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6509    0.6031    0.3162 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9355    1.9367    0.1063 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2054    2.3840   -0.2151 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1938    1.4308   -0.3199 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558    0.0893   -0.1190 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6649   -0.3122    0.2017 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3984   -1.7271    0.4145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0071   -2.1649    0.1106 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0357   -1.1273    0.0032 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2510   -1.6718    0.4579 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2089    1.8328   -0.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7201   -0.5595    0.0824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9279   -2.1508    0.3623 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8707    2.6081   -0.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6442    1.9643    0.9429 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3956    1.5194   -0.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2451    0.0532    1.7651 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1301    2.6428    0.1995 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4077    3.4530   -0.3779 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1865    1.7673   -0.5696 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7702   -0.6039   -0.2156 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6245   -1.9582    1.4898 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1378   -2.3144   -0.1699 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6715   -2.8996    0.8712 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.0169   -2.7117   -0.8566 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1875   -2.0379    1.5003 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4379   -2.5648   -0.1924 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  2  0
  5  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
  6  1  1  0
 17  8  1  0
 18  4  1  0
 14  9  1  0
  1 19  1  0
  2 20  1  0
  3 21  1  0
  6 22  1  0
  7 23  1  0
  7 24  1  0
  8 25  1  0
 10 26  1  0
 11 27  1  0
 12 28  1  0
 13 29  1  0
 15 30  1  0
 15 31  1  0
 16 32  1  0
 16 33  1  0
 18 34  1  0
 18 35  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
5,8,13,13a-Tetrahydro-6H-dibenzo[a,g]quinolizine	ChEBI
Tetrahydroprotoberberine	MeSH

Chemical Formula

C₁₇H₁₇N

Average Molecular Weight

235.33

Monoisotopic Molecular Weight

235.136099551

IUPAC Name

7,8,12b,13-tetrahydro-5H-6-azatetraphene

Traditional Name

berbine

CAS Registry Number

Not Available

SMILES

C1CC2=CC=CC=C2C2CC3=CC=CC=C3CN12

InChI Identifier

InChI=1S/C17H17N/c1-2-7-15-12-18-10-9-13-5-3-4-8-16(13)17(18)11-14(15)6-1/h1-8,17H,9-12H2

InChI Key

BRLDZKPJJNASGG-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

Tetrahydroprotoberberine skeleton
Protoberberine skeleton
Tetrahydroisoquinoline
Aralkylamine
Benzenoid
Tertiary aliphatic amine
Tertiary amine
Azacycle
Organoheterocyclic compound
Organic nitrogen compound
Organopnictogen compound
Hydrocarbon derivative
Organonitrogen compound
Amine
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

organic heterotetracyclic compound (CHEBI:35611 )
berberine alkaloid (CHEBI:35611 )
isoquinoline alkaloid fundamental parent (CHEBI:35611 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Non-excretory biofluid

Biofluid or Excreta

Blood (PMID: 31557052)

Source

Exogenous

Exogenous (PMID: 31557052)

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	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
logP	3.54	ALOGPS
logP	3.78	ChemAxon
logS	-4.2	ALOGPS
pKa (Strongest Basic)	6.73	ChemAxon
Physiological Charge	1	ChemAxon
Hydrogen Acceptor Count	1	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	3.24 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	75.5 m³·mol⁻¹	ChemAxon
Polarizability	27.83 Å³	ChemAxon
Number of Rings	4	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DeepCCS	[M-2H]-	184.103	30932474
DeepCCS	[M+Na]+	159.069	30932474
AllCCS	[M+H]+	157.8	32859911
AllCCS	[M+H-H2O]+	154.2	32859911
AllCCS	[M+NH4]+	161.2	32859911
AllCCS	[M+Na]+	162.2	32859911
AllCCS	[M-H]-	160.8	32859911
AllCCS	[M+Na-2H]-	160.0	32859911
AllCCS	[M+HCOO]-	159.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Berbine	C1CC2=CC=CC=C2C2CC3=CC=CC=C3CN12	3028.9	Standard polar	33892256
Berbine	C1CC2=CC=CC=C2C2CC3=CC=CC=C3CN12	1996.9	Standard non polar	33892256
Berbine	C1CC2=CC=CC=C2C2CC3=CC=CC=C3CN12	2191.2	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 - Berbine GC-MS (Non-derivatized) - 70eV, Positive	splash10-0zfr-0960000000-c3b020dab28ccee133a6	2021-09-24	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Berbine 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 - Berbine 10V, Positive-QTOF	splash10-000i-0090000000-499b4df711ddb6e0d0af	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbine 20V, Positive-QTOF	splash10-000i-0190000000-f04695cb2839ce0be9c6	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbine 40V, Positive-QTOF	splash10-0536-2920000000-73bd48df1b8479258718	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbine 10V, Negative-QTOF	splash10-001i-0090000000-d68b646d5174219194a2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbine 20V, Negative-QTOF	splash10-001i-0090000000-b461c4d69f2462811fce	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbine 40V, Negative-QTOF	splash10-001i-1490000000-0e1eec09fb23f81cf8a4	2021-10-12	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Blood

Tissue Locations

Not Available

Pathways

Not Available

Name	SMPDB/PathBank	KEGG

Normal Concentrations

Biospecimen	Status	Value	Age	Sex	Condition	Reference	Details
Blood	Detected but not Quantified	Not Quantified	Not Specified	Not Specified	Normal	31557052	details

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

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

35611

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for Berbine (HMDB0249085)

MOL for HMDB0249085 (Berbine)

3D MOL for HMDB0249085 (Berbine)

3D SDF for HMDB0249085 (Berbine)

3D-SDF for HMDB0249085 (Berbine)

PDB for HMDB0249085 (Berbine)

3D PDB for HMDB0249085 (Berbine)

SMILES for HMDB0249085 (Berbine)

INCHI for HMDB0249085 (Berbine)

Structure for HMDB0249085 (Berbine)

3D Structure for HMDB0249085 (Berbine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra