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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 18:32:39 UTC

Update Date

2022-03-07 02:53:51 UTC

HMDB ID

HMDB0033782

Secondary Accession Numbers

HMDB33782

Metabolite Identification

Common Name

Bergamottin

Description

Bergamottin is found in citrus. Bergamottin is a constituent of bergamot oil. Also from lemon oil and oils of other Citrus species and carrot (Daucus carota) Bergamottin is a natural furanocoumarin found principally in grapefruit juice. It is also found in the oil of bergamot, from which it was first isolated and from which its name is derived. To a lesser extent, bergamottin is also present in the essential oils of other citrus fruits. Along with the chemically related compound 6 ,7 -dihydroxybergamottin, it is believed to be responsible for the grapefruit juice effect in which the consumption of the juice affects the metabolism of a variety of pharmaceutical drugs

Structure

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

HMDB0033782
     RDKit          3D
Bergamottin
 47 49  0  0  0  0  0  0  0  0999 V2000
    6.4783    0.1946    0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1481    0.6209   -0.3378 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9164    2.0026   -0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1351   -0.2311   -0.3251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7984    0.1652   -0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7088    0.1218    0.2369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4150   -1.1697    0.8496 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4400   -1.8945    1.6883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2259   -1.7342    0.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9121   -1.1790   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0069   -1.0092    0.8726 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2021   -0.4931    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1739   -1.3274   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2418   -2.6981   -0.2317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4649   -2.9779   -0.7899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1065   -1.8569   -0.9920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3504   -0.8402   -0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5767    0.5189   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034    1.3561   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8713    2.6597   -0.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9903    3.5337    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2535    4.7626    0.2971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7767    3.1147    0.8290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4869    1.7673    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4234    0.8662    0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2824    0.3856   -0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5022   -0.9136    0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7487    0.6393    1.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5380    2.0114   -1.8777 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1036    2.4516   -0.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8536    2.6125   -0.7464 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2929   -1.2494    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053    1.2255   -1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5377   -0.4418   -1.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513    0.6714   -0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0861    0.7781    1.1011 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2070   -1.2174    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8801   -2.7459    1.1554 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8953   -2.2838    2.5857 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1130   -2.7218    1.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2338   -1.9983   -0.7532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7867   -0.2347   -0.5361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5156   -3.4485    0.0342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8464   -3.9668   -1.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5017    0.8947   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    3.8701    1.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5484    1.4084    1.2474 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 24 25  1  0
 25 12  1  0
 17 13  1  0
 25 19  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  8 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 14 43  1  0
 15 44  1  0
 18 45  1  0
 23 46  1  0
 24 47  1  0
M  END

Bergamottin
  Mrv1572001071617262D          

 25 27  0  0  0  0            999 V2000
   -2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    5.7750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9280    2.3174    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4130    1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9280    0.9826    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  5  4  1  0  0  0  0
  6  4  1  0  0  0  0
  8  7  2  0  0  0  0
 11  9  1  0  0  0  0
 12 10  2  0  0  0  0
 14  1  1  0  0  0  0
 14  2  1  0  0  0  0
 14  5  2  0  0  0  0
 15  3  1  0  0  0  0
 15  6  1  0  0  0  0
 15  9  2  0  0  0  0
 16  7  1  0  0  0  0
 17 10  1  0  0  0  0
 18 13  2  0  0  0  0
 18 17  1  0  0  0  0
 19 13  1  0  0  0  0
 19 16  2  0  0  0  0
 20  8  1  0  0  0  0
 21 16  1  0  0  0  0
 21 17  2  0  0  0  0
 22 20  2  0  0  0  0
 23 12  1  0  0  0  0
 23 18  1  0  0  0  0
 24 11  1  0  0  0  0
 24 21  1  0  0  0  0
 25 19  1  0  0  0  0
 25 20  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0033782

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCC\C(C)=C/COC1=C2C=COC2=CC2=C1C=CC(=O)O2

> <INCHI_IDENTIFIER>
InChI=1S/C21H22O4/c1-14(2)5-4-6-15(3)9-11-24-21-16-7-8-20(22)25-19(16)13-18-17(21)10-12-23-18/h5,7-10,12-13H,4,6,11H2,1-3H3/b15-9-

> <INCHI_KEY>
DBMJZOMNXBSRED-DHDCSXOGSA-N

> <FORMULA>
C21H22O4

> <MOLECULAR_WEIGHT>
338.403

> <EXACT_MASS>
338.151809188

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
47

> <JCHEM_AVERAGE_POLARIZABILITY>
37.47290220981984

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
5.30

> <JCHEM_LOGP>
4.805772115000001

> <ALOGPS_LOGS>
-4.51

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_BASIC>
-2.832524044388395

> <JCHEM_POLAR_SURFACE_AREA>
48.67

> <JCHEM_REFRACTIVITY>
99.77369999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.04e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}furo[3,2-g]chromen-7-one

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0033782
     RDKit          3D
Bergamottin
 47 49  0  0  0  0  0  0  0  0999 V2000
    6.4783    0.1946    0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1481    0.6209   -0.3378 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9164    2.0026   -0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1351   -0.2311   -0.3251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7984    0.1652   -0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7088    0.1218    0.2369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4150   -1.1697    0.8496 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4400   -1.8945    1.6883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2259   -1.7342    0.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9121   -1.1790   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0069   -1.0092    0.8726 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2021   -0.4931    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1739   -1.3274   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2418   -2.6981   -0.2317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4649   -2.9779   -0.7899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1065   -1.8569   -0.9920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3504   -0.8402   -0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5767    0.5189   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034    1.3561   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8713    2.6597   -0.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9903    3.5337    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2535    4.7626    0.2971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7767    3.1147    0.8290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4869    1.7673    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4234    0.8662    0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2824    0.3856   -0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5022   -0.9136    0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7487    0.6393    1.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5380    2.0114   -1.8777 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1036    2.4516   -0.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8536    2.6125   -0.7464 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2929   -1.2494    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053    1.2255   -1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5377   -0.4418   -1.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513    0.6714   -0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0861    0.7781    1.1011 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2070   -1.2174    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8801   -2.7459    1.1554 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8953   -2.2838    2.5857 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1130   -2.7218    1.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2338   -1.9983   -0.7532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7867   -0.2347   -0.5361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5156   -3.4485    0.0342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8464   -3.9668   -1.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5017    0.8947   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    3.8701    1.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5484    1.4084    1.2474 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 24 25  1  0
 25 12  1  0
 17 13  1  0
 25 19  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  8 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 14 43  1  0
 15 44  1  0
 18 45  1  0
 23 46  1  0
 24 47  1  0
M  END

HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Bergamottin                                       
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  C   UNK     0      -4.001   8.470   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.667  10.780   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  10.780   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.334   8.470   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   8.470   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   4.620   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.334   3.850   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.001   8.470   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       5.466   4.326   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       6.371   3.080   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.667   9.240   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   9.240   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       4.001   3.850   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      -1.334   2.310   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.667   4.620   0.000  0.00  0.00           C+0
HETATM   22  O   UNK     0      -2.667   1.540   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       5.466   1.834   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       2.667   6.160   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O+0
CONECT    1   14                                                            
CONECT    2   14                                                            
CONECT    3   15                                                            
CONECT    4    5    6                                                       
CONECT    5    4   14                                                       
CONECT    6    4   15                                                       
CONECT    7    8   16                                                       
CONECT    8    7   20                                                       
CONECT    9   11   15                                                       
CONECT   10   12   17                                                       
CONECT   11    9   24                                                       
CONECT   12   10   23                                                       
CONECT   13   18   19                                                       
CONECT   14    1    2    5                                                  
CONECT   15    3    6    9                                                  
CONECT   16    7   19   21                                                  
CONECT   17   10   18   21                                                  
CONECT   18   13   17   23                                                  
CONECT   19   13   16   25                                                  
CONECT   20    8   22   25                                                  
CONECT   21   16   17   24                                                  
CONECT   22   20                                                            
CONECT   23   12   18                                                       
CONECT   24   11   21                                                       
CONECT   25   19   20                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   54    0
END

COMPND    HMDB0033782
HETATM    1  C1  UNL     1       6.478   0.195   0.119  1.00  0.00           C  
HETATM    2  C2  UNL     1       5.148   0.621  -0.338  1.00  0.00           C  
HETATM    3  C3  UNL     1       4.916   2.003  -0.818  1.00  0.00           C  
HETATM    4  C4  UNL     1       4.135  -0.231  -0.325  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.798   0.165  -0.775  1.00  0.00           C  
HETATM    6  C6  UNL     1       1.709   0.122   0.237  1.00  0.00           C  
HETATM    7  C7  UNL     1       1.415  -1.170   0.850  1.00  0.00           C  
HETATM    8  C8  UNL     1       2.440  -1.894   1.688  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.226  -1.734   0.707  1.00  0.00           C  
HETATM   10  C10 UNL     1      -0.912  -1.179  -0.046  1.00  0.00           C  
HETATM   11  O1  UNL     1      -2.007  -1.009   0.873  1.00  0.00           O  
HETATM   12  C11 UNL     1      -3.202  -0.493   0.384  1.00  0.00           C  
HETATM   13  C12 UNL     1      -4.174  -1.327  -0.104  1.00  0.00           C  
HETATM   14  C13 UNL     1      -4.242  -2.698  -0.232  1.00  0.00           C  
HETATM   15  C14 UNL     1      -5.465  -2.978  -0.790  1.00  0.00           C  
HETATM   16  O2  UNL     1      -6.107  -1.857  -0.992  1.00  0.00           O  
HETATM   17  C15 UNL     1      -5.350  -0.840  -0.587  1.00  0.00           C  
HETATM   18  C16 UNL     1      -5.577   0.519  -0.589  1.00  0.00           C  
HETATM   19  C17 UNL     1      -4.603   1.356  -0.101  1.00  0.00           C  
HETATM   20  O3  UNL     1      -4.871   2.660  -0.125  1.00  0.00           O  
HETATM   21  C18 UNL     1      -3.990   3.534   0.325  1.00  0.00           C  
HETATM   22  O4  UNL     1      -4.254   4.763   0.297  1.00  0.00           O  
HETATM   23  C19 UNL     1      -2.777   3.115   0.829  1.00  0.00           C  
HETATM   24  C20 UNL     1      -2.487   1.767   0.860  1.00  0.00           C  
HETATM   25  C21 UNL     1      -3.423   0.866   0.384  1.00  0.00           C  
HETATM   26  H1  UNL     1       7.282   0.386  -0.636  1.00  0.00           H  
HETATM   27  H2  UNL     1       6.502  -0.914   0.283  1.00  0.00           H  
HETATM   28  H3  UNL     1       6.749   0.639   1.113  1.00  0.00           H  
HETATM   29  H4  UNL     1       4.538   2.011  -1.878  1.00  0.00           H  
HETATM   30  H5  UNL     1       4.104   2.452  -0.204  1.00  0.00           H  
HETATM   31  H6  UNL     1       5.854   2.613  -0.746  1.00  0.00           H  
HETATM   32  H7  UNL     1       4.293  -1.249   0.013  1.00  0.00           H  
HETATM   33  H8  UNL     1       2.805   1.225  -1.170  1.00  0.00           H  
HETATM   34  H9  UNL     1       2.538  -0.442  -1.672  1.00  0.00           H  
HETATM   35  H10 UNL     1       0.851   0.671  -0.188  1.00  0.00           H  
HETATM   36  H11 UNL     1       2.086   0.778   1.101  1.00  0.00           H  
HETATM   37  H12 UNL     1       3.207  -1.217   2.101  1.00  0.00           H  
HETATM   38  H13 UNL     1       2.880  -2.746   1.155  1.00  0.00           H  
HETATM   39  H14 UNL     1       1.895  -2.284   2.586  1.00  0.00           H  
HETATM   40  H15 UNL     1       0.113  -2.722   1.220  1.00  0.00           H  
HETATM   41  H16 UNL     1      -1.234  -1.998  -0.753  1.00  0.00           H  
HETATM   42  H17 UNL     1      -0.787  -0.235  -0.536  1.00  0.00           H  
HETATM   43  H18 UNL     1      -3.516  -3.448   0.034  1.00  0.00           H  
HETATM   44  H19 UNL     1      -5.846  -3.967  -1.029  1.00  0.00           H  
HETATM   45  H20 UNL     1      -6.502   0.895  -0.969  1.00  0.00           H  
HETATM   46  H21 UNL     1      -2.090   3.870   1.185  1.00  0.00           H  
HETATM   47  H22 UNL     1      -1.548   1.408   1.247  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3    4    4
CONECT    3   29   30   31
CONECT    4    5   32
CONECT    5    6   33   34
CONECT    6    7   35   36
CONECT    7    8    9    9
CONECT    8   37   38   39
CONECT    9   10   40
CONECT   10   11   41   42
CONECT   11   12
CONECT   12   13   13   25
CONECT   13   14   17
CONECT   14   15   15   43
CONECT   15   16   44
CONECT   16   17
CONECT   17   18   18
CONECT   18   19   45
CONECT   19   20   25   25
CONECT   20   21
CONECT   21   22   22   23
CONECT   23   24   24   46
CONECT   24   25   47
END

HMDB0033782
     RDKit          3D
Bergamottin
 47 49  0  0  0  0  0  0  0  0999 V2000
    6.4783    0.1946    0.1195 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1481    0.6209   -0.3378 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9164    2.0026   -0.8183 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1351   -0.2311   -0.3251 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7984    0.1652   -0.7748 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7088    0.1218    0.2369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4150   -1.1697    0.8496 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4400   -1.8945    1.6883 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2259   -1.7342    0.7074 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9121   -1.1790   -0.0457 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0069   -1.0092    0.8726 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2021   -0.4931    0.3836 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1739   -1.3274   -0.1037 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2418   -2.6981   -0.2317 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4649   -2.9779   -0.7899 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1065   -1.8569   -0.9920 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3504   -0.8402   -0.5866 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5767    0.5189   -0.5889 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6034    1.3561   -0.1007 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8713    2.6597   -0.1253 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9903    3.5337    0.3250 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2535    4.7626    0.2971 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7767    3.1147    0.8290 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4869    1.7673    0.8601 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4234    0.8662    0.3835 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2824    0.3856   -0.6356 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5022   -0.9136    0.2834 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7487    0.6393    1.1127 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5380    2.0114   -1.8777 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1036    2.4516   -0.2044 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8536    2.6125   -0.7464 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2929   -1.2494    0.0125 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8053    1.2255   -1.1701 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5377   -0.4418   -1.6718 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8513    0.6714   -0.1884 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0861    0.7781    1.1011 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2070   -1.2174    2.1009 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8801   -2.7459    1.1554 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8953   -2.2838    2.5857 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1130   -2.7218    1.2198 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2338   -1.9983   -0.7532 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7867   -0.2347   -0.5361 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5156   -3.4485    0.0342 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8464   -3.9668   -1.0286 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5017    0.8947   -0.9691 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0897    3.8701    1.1853 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5484    1.4084    1.2474 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  2  3
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 13 14  1  0
 14 15  2  0
 15 16  1  0
 16 17  1  0
 17 18  2  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  2  0
 24 25  1  0
 25 12  1  0
 17 13  1  0
 25 19  2  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  3 29  1  0
  3 30  1  0
  3 31  1  0
  4 32  1  0
  5 33  1  0
  5 34  1  0
  6 35  1  0
  6 36  1  0
  8 37  1  0
  8 38  1  0
  8 39  1  0
  9 40  1  0
 10 41  1  0
 10 42  1  0
 14 43  1  0
 15 44  1  0
 18 45  1  0
 23 46  1  0
 24 47  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
4-[(3,7-Dimethyl-2,6-octadienyl)oxy]-7H-furo[3,2-g][1]benzopyran-7-one, 9ci	HMDB
5-Geranoxypsoralen	HMDB
5-Geranyloxypsoralen	HMDB
Bergamotin	HMDB
Bergamotine	HMDB
Bergaptin	HMDB
Bergaptol geranyl ether	HMDB

Chemical Formula

C₂₁H₂₂O₄

Average Molecular Weight

338.403

Monoisotopic Molecular Weight

338.151809188

IUPAC Name

4-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}-7H-furo[3,2-g]chromen-7-one

Traditional Name

4-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}furo[3,2-g]chromen-7-one

CAS Registry Number

7380-40-7

SMILES

CC(C)=CCC\C(C)=C/COC1=C2C=COC2=CC2=C1C=CC(=O)O2

InChI Identifier

InChI=1S/C21H22O4/c1-14(2)5-4-6-15(3)9-11-24-21-16-7-8-20(22)25-19(16)13-18-17(21)10-12-23-18/h5,7-10,12-13H,4,6,11H2,1-3H3/b15-9-

InChI Key

DBMJZOMNXBSRED-DHDCSXOGSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as terpene lactones. These are prenol lipids containing a lactone ring.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Prenol lipids

Sub Class

Terpene lactones

Direct Parent

Terpene lactones

Alternative Parents

Substituents

Terpene lactone
Linear furanocoumarin
Furanocoumarin
Psoralen
Coumarin
Benzopyran
1-benzopyran
Monoterpenoid
Aromatic monoterpenoid
Benzofuran
Alkyl aryl ether
Pyranone
Benzenoid
Pyran
Furan
Heteroaromatic compound
Lactone
Oxacycle
Organoheterocyclic compound
Ether
Organic oxygen compound
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0033782)

Membrane (HMDB: HMDB0033782)
Cell membrane (HMDB: HMDB0033782)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0033782)

Source

Exogenous

Food

Food (HMDB: HMDB0033782)

Fruit

Citrus

Grapefruit (FooDB: FOOD00256)
Lemon (FooDB: FOOD00054)
Lime (FooDB: FOOD00053)
Citrus (FooDB: FOOD00859)
Pummelo (FooDB: FOOD00055)

Tea

Black tea (FooDB: FOOD00907)

Vegetable

Root vegetable

Root vegetables (FooDB: FOOD00873)

Endogenous

Plant

Plant (HMDB: HMDB0033782)

Not Available

Nutrient (HMDB: HMDB0033782)

calcium antagonist (HMDB: HMDB0033782)

Modulator

Inhibitor

Enzyme inhibitor

cytochrome-P450 inhibitor (HMDB: HMDB0033782)

Industrial application

Pharmaceutical industry

Antineoplastic agent

Antitumor (HMDB: HMDB0033782)

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	59 - 61 °C	Not Available
Boiling Point	503.00 to 504.00 °C. @ 760.00 mm Hg (est)	The Good Scents Company Information System
Water Solubility	0.034 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	5.382 (est)	The Good Scents Company Information System

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.01 g/L	ALOGPS
logP	5.3	ALOGPS
logP	4.81	ChemAxon
logS	-4.5	ALOGPS
pKa (Strongest Basic)	-2.8	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	2	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	48.67 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	99.77 m³·mol⁻¹	ChemAxon
Polarizability	37.47 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	180.773	31661259
DarkChem	[M-H]-	179.04	31661259
DeepCCS	[M+H]+	182.584	30932474
DeepCCS	[M-H]-	180.226	30932474
DeepCCS	[M-2H]-	213.568	30932474
DeepCCS	[M+Na]+	188.848	30932474
AllCCS	[M+H]+	182.0	32859911
AllCCS	[M+H-H2O]+	179.0	32859911
AllCCS	[M+NH4]+	184.8	32859911
AllCCS	[M+Na]+	185.6	32859911
AllCCS	[M-H]-	185.7	32859911
AllCCS	[M+Na-2H]-	185.0	32859911
AllCCS	[M+HCOO]-	184.4	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Bergamottin	CC(C)=CCC\C(C)=C/COC1=C2C=COC2=CC2=C1C=CC(=O)O2	3648.3	Standard polar	33892256
Bergamottin	CC(C)=CCC\C(C)=C/COC1=C2C=COC2=CC2=C1C=CC(=O)O2	2816.9	Standard non polar	33892256
Bergamottin	CC(C)=CCC\C(C)=C/COC1=C2C=COC2=CC2=C1C=CC(=O)O2	2911.7	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 - Bergamottin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0gi0-9563000000-1489fb332877b9483715	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bergamottin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Bergamottin 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 - Bergamottin 10V, Positive-QTOF	splash10-000i-1449000000-f1cb80e88623323efd78	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 20V, Positive-QTOF	splash10-00kr-7974000000-8dc8885c8ce63b6b8f05	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 40V, Positive-QTOF	splash10-0uxr-9420000000-d4a732b567f78ee66d36	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 10V, Negative-QTOF	splash10-000i-0059000000-6c5381fc4c44ea7b815b	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 20V, Negative-QTOF	splash10-0udi-0392000000-aef5d498f581369a1495	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 40V, Negative-QTOF	splash10-0a4i-0910000000-f3479b11ac7337bdd5d4	2017-06-28	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 10V, Positive-QTOF	splash10-0udi-0090000000-2e5a86e101fa40f235c9	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 20V, Positive-QTOF	splash10-0udi-1090000000-f45a823c8a5c19aa4914	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 40V, Positive-QTOF	splash10-0fb9-6960000000-6c6cb6ea0377f6b535b7	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 10V, Negative-QTOF	splash10-000i-0019000000-3816dc9471dd695014e5	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 20V, Negative-QTOF	splash10-000i-1897000000-825739cf6e0dc17d5b81	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Bergamottin 40V, Negative-QTOF	splash10-0zfr-2980000000-b70406757f87828a48a0	2021-09-22	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Membrane

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

FDB011939

KNApSAcK ID

C00047753

Chemspider ID

5584831

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Bergamottin

METLIN ID

Not Available

PubChem Compound

7251175

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1012211

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Hwang YP, Yun HJ, Choi JH, Kang KW, Jeong HG: Suppression of phorbol-12-myristate-13-acetate-induced tumor cell invasion by bergamottin via the inhibition of protein kinase Cdelta/p38 mitogen-activated protein kinase and JNK/nuclear factor-kappaB-dependent matrix metalloproteinase-9 expression. Mol Nutr Food Res. 2010 Jul;54(7):977-90. doi: 10.1002/mnfr.200900283. [PubMed:19943262 ]
(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Bergamottin (HMDB0033782)

MOL for HMDB0033782 (Bergamottin)

3D MOL for HMDB0033782 (Bergamottin)

3D SDF for HMDB0033782 (Bergamottin)

3D-SDF for HMDB0033782 (Bergamottin)

PDB for HMDB0033782 (Bergamottin)

3D PDB for HMDB0033782 (Bergamottin)

SMILES for HMDB0033782 (Bergamottin)

INCHI for HMDB0033782 (Bergamottin)

Structure for HMDB0033782 (Bergamottin)

3D Structure for HMDB0033782 (Bergamottin)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

GC-MS Spectra

MS/MS Spectra