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Record Information

Version

5.0

Status

Detected but not Quantified

Creation Date

2021-09-07 01:48:44 UTC

Update Date

2022-11-23 21:48:33 UTC

HMDB ID

HMDB0242681

Secondary Accession Numbers

None

Metabolite Identification

Common Name

Berbamine

Description

BERBAMINE belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed. Based on a literature review a significant number of articles have been published on BERBAMINE. This compound has been identified in human blood as reported by (PMID: 31557052 ). Berbamine is not a naturally occurring metabolite and is only found in those individuals exposed to this compound or its derivatives. Technically Berbamine 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

  Mrv1533004171516082D          

 45 51  0  0  0  0            999 V2000
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    0.6741   -4.6557    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7208   -3.8320    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0105   -3.3943    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0266   -2.5532    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6813   -2.0942    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6618   -1.2636    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0684   -0.8735    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
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    0.7936   -1.2970    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.5545   -0.4105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  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  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  8 10  1  0  0  0  0
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  5 38  2  0  0  0  0
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 15 44  1  0  0  0  0
 44 45  2  0  0  0  0
 12 45  1  0  0  0  0
M  END

HMDB0242681
     RDKit          3D
BERBAMINE
 85 91  0  0  0  0  0  0  0  0999 V2000
    0.2501   -2.6056   -3.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

  Mrv1533004171516082D          

 45 51  0  0  0  0            999 V2000
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    5.9856   -0.9369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3161   -0.1810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2994    0.5897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4640    0.5625    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  1  0  0  0  0
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 21 22  1  0  0  0  0
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 44 45  2  0  0  0  0
 12 45  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0242681

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC2=C3C=C1OC1=C4C(CC5=CC=C(O)C(OC6=CC=C(CC3N(C)CC2)C=C6)=C5)N(C)CCC4=CC(OC)=C1OC

> <INCHI_IDENTIFIER>
InChI=1S/C37H40N2O6/c1-38-14-12-24-19-32(41-3)33-21-27(24)28(38)16-22-6-9-26(10-7-22)44-31-18-23(8-11-30(31)40)17-29-35-25(13-15-39(29)2)20-34(42-4)36(43-5)37(35)45-33/h6-11,18-21,28-29,40H,12-17H2,1-5H3

> <INCHI_KEY>
DFOCUWZXJBAUSQ-UHFFFAOYSA-N

> <FORMULA>
C37H40N2O6

> <MOLECULAR_WEIGHT>
608.735

> <EXACT_MASS>
608.288637016

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
85

> <JCHEM_AVERAGE_POLARIZABILITY>
66.73257331447027

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
20,21,25-trimethoxy-15,30-dimethyl-7,23-dioxa-15,30-diazaheptacyclo[22.6.2.2³,⁶.1⁸,¹².1¹⁴,¹⁸.0²⁷,³¹.0²²,³³]hexatriaconta-3,5,8(34),9,11,18,20,22(33),24(32),25,27(31),35-dodecaen-9-ol

> <ALOGPS_LOGP>
5.54

> <JCHEM_LOGP>
5.760934809499735

> <ALOGPS_LOGS>
-4.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
7

> <JCHEM_PHYSIOLOGICAL_CHARGE>
2

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.869299069283281

> <JCHEM_PKA_STRONGEST_BASIC>
8.223023732142078

> <JCHEM_POLAR_SURFACE_AREA>
72.86000000000001

> <JCHEM_REFRACTIVITY>
175.63229999999993

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.48e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
berbamine

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0242681
     RDKit          3D
BERBAMINE
 85 91  0  0  0  0  0  0  0  0999 V2000
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M  END

HEADER    PROTEIN                                 17-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-APR-15         0                                  
HETATM    1  C   UNK     0      -0.117  -9.384   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.258  -8.691   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0       1.346  -7.153   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.020  -6.336   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.050  -4.766   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.272  -3.909   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.235  -2.359   0.000  0.00  0.00           C+0
HETATM    8  N   UNK     0       0.128  -1.631   0.000  0.00  0.00           N+0
HETATM    9  C   UNK     0       0.157  -0.091   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.481  -2.421   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.504  -1.190   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.843  -0.328   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       4.694  -1.634   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.230  -1.589   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.002  -0.228   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       8.502  -0.766   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       9.610  -1.907   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       9.037  -3.375   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       9.916  -4.674   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       9.003  -6.022   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       8.395  -7.546   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0       9.859  -8.115   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      11.035  -7.122   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      10.169  -9.628   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       9.005 -10.642   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       7.517 -10.152   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0       6.417 -11.268   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0       4.919 -10.891   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0       3.844 -11.994   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0       2.352 -11.615   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       4.505  -9.406   0.000  0.00  0.00           C+0
HETATM   32  O   UNK     0       3.004  -9.062   0.000  0.00  0.00           O+0
HETATM   33  C   UNK     0       1.956 -10.190   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       5.542  -8.229   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       4.244  -7.211   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       2.775  -6.482   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       2.753  -4.910   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       1.435  -4.025   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0       7.146  -8.608   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      11.478  -4.416   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      12.108  -2.989   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      11.173  -1.749   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      11.790  -0.338   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0       6.159   1.101   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       4.599   1.050   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4   36                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6   38                                                  
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9   10                                                  
CONECT    9    8                                                            
CONECT   10    8   11   38                                                  
CONECT   11   10   12                                                       
CONECT   12   11   13   45                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   44                                                  
CONECT   16   15   17                                                       
CONECT   17   16   18   42                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20   40                                                  
CONECT   20   19   21                                                       
CONECT   21   20   22   39                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   39                                                  
CONECT   27   26   28                                                       
CONECT   28   27   29   31                                                  
CONECT   29   28   30                                                       
CONECT   30   29                                                            
CONECT   31   28   32   34                                                  
CONECT   32   31   33                                                       
CONECT   33   32                                                            
CONECT   34   31   35   39                                                  
CONECT   35   34   36                                                       
CONECT   36   35    3   37                                                  
CONECT   37   36   38                                                       
CONECT   38   37    5   10                                                  
CONECT   39   34   21   26                                                  
CONECT   40   19   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   17   43                                                  
CONECT   43   42                                                            
CONECT   44   15   45                                                       
CONECT   45   44   12                                                       
MASTER        0    0    0    0    0    0    0    0   45    0  102    0
END

COMPND    HMDB0242681
HETATM    1  C1  UNL     1       0.250  -2.606  -3.611  1.00  0.00           C  
HETATM    2  O1  UNL     1       0.082  -1.949  -2.402  1.00  0.00           O  
HETATM    3  C2  UNL     1       1.123  -1.462  -1.587  1.00  0.00           C  
HETATM    4  C3  UNL     1       2.369  -1.712  -2.126  1.00  0.00           C  
HETATM    5  C4  UNL     1       3.422  -1.265  -1.395  1.00  0.00           C  
HETATM    6  C5  UNL     1       3.287  -0.567  -0.138  1.00  0.00           C  
HETATM    7  C6  UNL     1       2.052  -0.346   0.363  1.00  0.00           C  
HETATM    8  C7  UNL     1       0.916  -0.798  -0.368  1.00  0.00           C  
HETATM    9  O2  UNL     1      -0.365  -0.624   0.050  1.00  0.00           O  
HETATM   10  C8  UNL     1      -1.502  -0.923   0.692  1.00  0.00           C  
HETATM   11  C9  UNL     1      -1.683  -1.520   1.931  1.00  0.00           C  
HETATM   12  O3  UNL     1      -0.571  -1.892   2.735  1.00  0.00           O  
HETATM   13  C10 UNL     1      -0.034  -3.167   2.574  1.00  0.00           C  
HETATM   14  C11 UNL     1      -2.899  -1.813   2.521  1.00  0.00           C  
HETATM   15  O4  UNL     1      -2.952  -2.419   3.783  1.00  0.00           O  
HETATM   16  C12 UNL     1      -4.168  -2.728   4.411  1.00  0.00           C  
HETATM   17  C13 UNL     1      -4.040  -1.493   1.832  1.00  0.00           C  
HETATM   18  C14 UNL     1      -3.962  -0.888   0.580  1.00  0.00           C  
HETATM   19  C15 UNL     1      -2.740  -0.623   0.064  1.00  0.00           C  
HETATM   20  C16 UNL     1      -2.801   0.178  -1.223  1.00  0.00           C  
HETATM   21  C17 UNL     1      -3.257   1.561  -1.000  1.00  0.00           C  
HETATM   22  C18 UNL     1      -2.406   2.697  -0.615  1.00  0.00           C  
HETATM   23  C19 UNL     1      -3.236   3.838  -0.385  1.00  0.00           C  
HETATM   24  C20 UNL     1      -2.816   5.055   0.026  1.00  0.00           C  
HETATM   25  C21 UNL     1      -1.453   5.157   0.232  1.00  0.00           C  
HETATM   26  O5  UNL     1      -1.031   6.431   0.661  1.00  0.00           O  
HETATM   27  C22 UNL     1      -0.600   4.084   0.025  1.00  0.00           C  
HETATM   28  C23 UNL     1      -1.055   2.860  -0.397  1.00  0.00           C  
HETATM   29  O6  UNL     1       0.718   4.498   0.329  1.00  0.00           O  
HETATM   30  C24 UNL     1       1.851   3.672   0.554  1.00  0.00           C  
HETATM   31  C25 UNL     1       2.715   3.369  -0.442  1.00  0.00           C  
HETATM   32  C26 UNL     1       3.829   2.507  -0.245  1.00  0.00           C  
HETATM   33  C27 UNL     1       4.032   1.960   0.997  1.00  0.00           C  
HETATM   34  C28 UNL     1       3.152   2.293   1.998  1.00  0.00           C  
HETATM   35  C29 UNL     1       2.034   3.167   1.784  1.00  0.00           C  
HETATM   36  C30 UNL     1       5.074   0.829   1.187  1.00  0.00           C  
HETATM   37  C31 UNL     1       4.668  -0.213   0.237  1.00  0.00           C  
HETATM   38  N1  UNL     1       5.362  -1.440   0.492  1.00  0.00           N  
HETATM   39  C32 UNL     1       4.572  -2.363   1.290  1.00  0.00           C  
HETATM   40  C33 UNL     1       5.698  -2.073  -0.749  1.00  0.00           C  
HETATM   41  C34 UNL     1       4.826  -1.572  -1.853  1.00  0.00           C  
HETATM   42  N2  UNL     1      -3.712  -0.585  -2.040  1.00  0.00           N  
HETATM   43  C35 UNL     1      -3.517  -0.451  -3.438  1.00  0.00           C  
HETATM   44  C36 UNL     1      -5.077  -0.511  -1.611  1.00  0.00           C  
HETATM   45  C37 UNL     1      -5.260  -0.658  -0.151  1.00  0.00           C  
HETATM   46  H1  UNL     1      -0.751  -2.967  -3.955  1.00  0.00           H  
HETATM   47  H2  UNL     1       0.712  -1.890  -4.334  1.00  0.00           H  
HETATM   48  H3  UNL     1       0.935  -3.479  -3.446  1.00  0.00           H  
HETATM   49  H4  UNL     1       2.490  -2.238  -3.086  1.00  0.00           H  
HETATM   50  H5  UNL     1       1.835   0.145   1.362  1.00  0.00           H  
HETATM   51  H6  UNL     1      -0.147  -3.706   3.547  1.00  0.00           H  
HETATM   52  H7  UNL     1       1.061  -3.033   2.328  1.00  0.00           H  
HETATM   53  H8  UNL     1      -0.553  -3.680   1.745  1.00  0.00           H  
HETATM   54  H9  UNL     1      -4.907  -3.157   3.705  1.00  0.00           H  
HETATM   55  H10 UNL     1      -4.656  -1.810   4.844  1.00  0.00           H  
HETATM   56  H11 UNL     1      -4.025  -3.492   5.221  1.00  0.00           H  
HETATM   57  H12 UNL     1      -5.014  -1.715   2.264  1.00  0.00           H  
HETATM   58  H13 UNL     1      -1.816   0.141  -1.698  1.00  0.00           H  
HETATM   59  H14 UNL     1      -4.138   1.519  -0.219  1.00  0.00           H  
HETATM   60  H15 UNL     1      -3.890   1.814  -1.910  1.00  0.00           H  
HETATM   61  H16 UNL     1      -4.333   3.736  -0.558  1.00  0.00           H  
HETATM   62  H17 UNL     1      -3.483   5.901   0.191  1.00  0.00           H  
HETATM   63  H18 UNL     1      -0.060   6.587   0.831  1.00  0.00           H  
HETATM   64  H19 UNL     1      -0.352   1.988  -0.605  1.00  0.00           H  
HETATM   65  H20 UNL     1       2.698   3.737  -1.513  1.00  0.00           H  
HETATM   66  H21 UNL     1       4.408   2.488  -1.223  1.00  0.00           H  
HETATM   67  H22 UNL     1       3.101   2.030   3.090  1.00  0.00           H  
HETATM   68  H23 UNL     1       1.442   3.334   2.743  1.00  0.00           H  
HETATM   69  H24 UNL     1       5.208   0.454   2.207  1.00  0.00           H  
HETATM   70  H25 UNL     1       6.117   1.164   0.986  1.00  0.00           H  
HETATM   71  H26 UNL     1       5.225   0.181  -0.737  1.00  0.00           H  
HETATM   72  H27 UNL     1       4.199  -3.170   0.633  1.00  0.00           H  
HETATM   73  H28 UNL     1       3.724  -1.829   1.804  1.00  0.00           H  
HETATM   74  H29 UNL     1       5.137  -2.839   2.094  1.00  0.00           H  
HETATM   75  H30 UNL     1       6.766  -1.862  -1.040  1.00  0.00           H  
HETATM   76  H31 UNL     1       5.536  -3.169  -0.650  1.00  0.00           H  
HETATM   77  H32 UNL     1       5.276  -0.730  -2.371  1.00  0.00           H  
HETATM   78  H33 UNL     1       4.693  -2.369  -2.651  1.00  0.00           H  
HETATM   79  H34 UNL     1      -2.564  -0.910  -3.779  1.00  0.00           H  
HETATM   80  H35 UNL     1      -4.409  -0.830  -3.981  1.00  0.00           H  
HETATM   81  H36 UNL     1      -3.452   0.634  -3.675  1.00  0.00           H  
HETATM   82  H37 UNL     1      -5.582  -1.386  -2.121  1.00  0.00           H  
HETATM   83  H38 UNL     1      -5.605   0.369  -2.035  1.00  0.00           H  
HETATM   84  H39 UNL     1      -5.809   0.126   0.385  1.00  0.00           H  
HETATM   85  H40 UNL     1      -5.914  -1.580   0.035  1.00  0.00           H  
CONECT    1    2   46   47   48
CONECT    2    3
CONECT    3    4    4    8
CONECT    4    5   49
CONECT    5    6    6   41
CONECT    6    7   37
CONECT    7    8    8   50
CONECT    8    9
CONECT    9   10
CONECT   10   11   11   19
CONECT   11   12   14
CONECT   12   13
CONECT   13   51   52   53
CONECT   14   15   17   17
CONECT   15   16
CONECT   16   54   55   56
CONECT   17   18   57
CONECT   18   19   19   45
CONECT   19   20
CONECT   20   21   42   58
CONECT   21   22   59   60
CONECT   22   23   23   28
CONECT   23   24   61
CONECT   24   25   25   62
CONECT   25   26   27
CONECT   26   63
CONECT   27   28   28   29
CONECT   28   64
CONECT   29   30
CONECT   30   31   31   35
CONECT   31   32   65
CONECT   32   33   33   66
CONECT   33   34   36
CONECT   34   35   35   67
CONECT   35   68
CONECT   36   37   69   70
CONECT   37   38   71
CONECT   38   39   40
CONECT   39   72   73   74
CONECT   40   41   75   76
CONECT   41   77   78
CONECT   42   43   44
CONECT   43   79   80   81
CONECT   44   45   82   83
CONECT   45   84   85
END

HMDB0242681
     RDKit          3D
BERBAMINE
 85 91  0  0  0  0  0  0  0  0999 V2000
    0.2501   -2.6056   -3.6114 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0820   -1.9492   -2.4019 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1229   -1.4624   -1.5871 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.3685   -1.7118   -2.1259 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4224   -1.2645   -1.3953 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2872   -0.5673   -0.1380 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0517   -0.3456    0.3628 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9157   -0.7984   -0.3684 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3650   -0.6238    0.0503 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5024   -0.9232    0.6920 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6834   -1.5200    1.9305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5712   -1.8925    2.7347 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0340   -3.1667    2.5736 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8989   -1.8134    2.5206 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9519   -2.4187    3.7832 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1675   -2.7283    4.4109 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0404   -1.4934    1.8320 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9618   -0.8882    0.5799 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7404   -0.6232    0.0640 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8005    0.1782   -1.2230 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2569    1.5607   -1.0001 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4055    2.6975   -0.6147 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2364    3.8382   -0.3845 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8164    5.0546    0.0264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4534    5.1574    0.2319 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0308    6.4307    0.6610 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5997    4.0839    0.0252 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0553    2.8595   -0.3969 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7180    4.4984    0.3290 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.8513    3.6717    0.5538 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7154    3.3693   -0.4421 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8291    2.5070   -0.2451 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0316    1.9598    0.9973 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1521    2.2934    1.9983 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0345    3.1668    1.7843 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0740    0.8288    1.1871 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6682   -0.2131    0.2371 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3622   -1.4400    0.4925 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.5723   -2.3635    1.2902 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6981   -2.0730   -0.7490 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8255   -1.5721   -1.8531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7120   -0.5850   -2.0402 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5169   -0.4507   -3.4380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0767   -0.5108   -1.6108 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2596   -0.6584   -0.1505 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7507   -2.9670   -3.9546 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7122   -1.8904   -4.3335 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9354   -3.4793   -3.4461 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4902   -2.2376   -3.0860 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8348    0.1452    1.3618 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.5528   -3.6796    1.7453 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.0254   -3.4924    5.2206 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1174    1.1642    0.9864 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2252    0.1810   -0.7368 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1985   -3.1701    0.6327 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7236   -1.8290    1.8037 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1372   -2.8391    2.0939 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7659   -1.8621   -1.0396 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5363   -3.1692   -0.6504 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2759   -0.7299   -2.3714 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6928   -2.3692   -2.6508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5641   -0.9104   -3.7789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4089   -0.8303   -3.9810 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4521    0.6336   -3.6753 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5825   -1.3862   -2.1214 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.8088    0.1263    0.3852 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9143   -1.5802    0.0353 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
6,6',7-Trimethoxy-2,2'-dimethylberbaman-12-ol	HMDB
Berbamine dihydrochloride	HMDB
Berbamine, (1'beta)-isomer	HMDB
Berbamine, (1beta)-isomer	HMDB
Berbamine hydrochloride	HMDB
Berbamine monohydrochloride	HMDB

Chemical Formula

C₃₇H₄₀N₂O₆

Average Molecular Weight

608.735

Monoisotopic Molecular Weight

608.288637016

IUPAC Name

20,21,25-trimethoxy-15,30-dimethyl-7,23-dioxa-15,30-diazaheptacyclo[22.6.2.2³,⁶.1⁸,¹².1¹⁴,¹⁸.0²⁷,³¹.0²²,³³]hexatriaconta-3,5,8(34),9,11,18,20,22(33),24(32),25,27(31),35-dodecaen-9-ol

Traditional Name

berbamine

CAS Registry Number

Not Available

SMILES

COC1=CC2=C3C=C1OC1=C4C(CC5=CC=C(O)C(OC6=CC=C(CC3N(C)CC2)C=C6)=C5)N(C)CCC4=CC(OC)=C1OC

InChI Identifier

InChI=1S/C37H40N2O6/c1-38-14-12-24-19-32(41-3)33-21-27(24)28(38)16-22-6-9-26(10-7-22)44-31-18-23(8-11-30(31)40)17-29-35-25(13-15-39(29)2)20-34(42-4)36(43-5)37(35)45-33/h6-11,18-21,28-29,40H,12-17H2,1-5H3

InChI Key

DFOCUWZXJBAUSQ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as lignans, neolignans and related compounds. These are plant products of low molecular weight formed primarily from oxidative coupling of two p-propylphenol moieties. They can also be described as micromolecules with two phenylpropanoid units coupled together. They can be attached in various manners, like C5-C5', C8-C8'. Most known natural lignans are oxidized at C9 and C9´ and, based upon the way in which oxygen is incorporated into the skeleton and on the cyclization patterns, a wide range of lignans of very different structural types can be formed.

Kingdom

Organic compounds

Super Class

Lignans, neolignans and related compounds

Class

Not Available

Sub Class

Not Available

Direct Parent

Lignans, neolignans and related compounds

Alternative Parents

Substituents

Oxyneolignan skeleton
Diaryl ether
Tetrahydroisoquinoline
Anisole
Alkyl aryl ether
1-hydroxy-2-unsubstituted benzenoid
Aralkylamine
Benzenoid
Tertiary amine
Tertiary aliphatic amine
Ether
Oxacycle
Azacycle
Organoheterocyclic compound
Organonitrogen compound
Hydrocarbon derivative
Organic nitrogen compound
Organopnictogen compound
Organooxygen compound
Amine
Organic oxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

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	5.54	ALOGPS
logP	5.76	ChemAxon
logS	-4.9	ALOGPS
pKa (Strongest Acidic)	8.87	ChemAxon
pKa (Strongest Basic)	8.22	ChemAxon
Physiological Charge	2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	72.86 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	175.63 m³·mol⁻¹	ChemAxon
Polarizability	66.73 Å³	ChemAxon
Number of Rings	7	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	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]+	245.527	30932474
DeepCCS	[M-H]-	243.255	30932474
DeepCCS	[M-2H]-	276.496	30932474
DeepCCS	[M+Na]+	251.439	30932474
AllCCS	[M+H]+	247.3	32859911
AllCCS	[M+H-H2O]+	246.3	32859911
AllCCS	[M+NH4]+	248.2	32859911
AllCCS	[M+Na]+	248.5	32859911
AllCCS	[M-H]-	220.4	32859911
AllCCS	[M+Na-2H]-	221.2	32859911
AllCCS	[M+HCOO]-	222.3	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
BERBAMINE	COC1=CC2=C3C=C1OC1=C4C(CC5=CC=C(O)C(OC6=CC=C(CC3N(C)CC2)C=C6)=C5)N(C)CCC4=CC(OC)=C1OC	5646.3	Standard polar	33892256
BERBAMINE	COC1=CC2=C3C=C1OC1=C4C(CC5=CC=C(O)C(OC6=CC=C(CC3N(C)CC2)C=C6)=C5)N(C)CCC4=CC(OC)=C1OC	4566.0	Standard non polar	33892256
BERBAMINE	COC1=CC2=C3C=C1OC1=C4C(CC5=CC=C(O)C(OC6=CC=C(CC3N(C)CC2)C=C6)=C5)N(C)CCC4=CC(OC)=C1OC	4685.9	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 - Berbamine GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-03	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Berbamine GC-MS (TBDMS_1_1) - 70eV, Positive	Not Available	2021-11-03	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 - Berbamine 10V, Positive-QTOF	splash10-0a4i-0000019000-333540c4f603927a74d7	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbamine 20V, Positive-QTOF	splash10-05rr-0000091000-921792f714c7b476fde2	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbamine 40V, Positive-QTOF	splash10-0fuu-1000090000-6c32f06e6b528e79eef3	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbamine 10V, Negative-QTOF	splash10-0a4i-0000009000-243a991931ec2986982a	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbamine 20V, Negative-QTOF	splash10-0a4i-0000069000-72889e1adced7287ce1b	2021-10-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Berbamine 40V, Negative-QTOF	splash10-06r2-0000090000-71540da15bceabf0838f	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

C00001817

Chemspider ID

9764

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

10170

PDB ID

Not Available

ChEBI ID

Not Available

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 Berbamine (HMDB0242681)

MOL for HMDB0242681 (Berbamine)

3D MOL for HMDB0242681 (Berbamine)

3D SDF for HMDB0242681 (Berbamine)

3D-SDF for HMDB0242681 (Berbamine)

PDB for HMDB0242681 (Berbamine)

3D PDB for HMDB0242681 (Berbamine)

SMILES for HMDB0242681 (Berbamine)

INCHI for HMDB0242681 (Berbamine)

Structure for HMDB0242681 (Berbamine)

3D Structure for HMDB0242681 (Berbamine)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra