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Showing metabocard for Bergaptol (HMDB0013679)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-04-03 14:10:31 UTC
Update Date2023-02-21 17:18:01 UTC
HMDB IDHMDB0013679
Secondary Accession Numbers
  • HMDB13679
Metabolite Identification
Common NameBergaptol
DescriptionBergaptol, also known as 5-hydroxypsoralen, belongs to the class of organic compounds known as 5-hydroxypsoralens. These are psoralens containing a hydroxyl group attached at the C5 position of the psoralen group. Bergaptol has been detected, but not quantified in, several different foods, such as spinaches (Spinacia oleracea), sugar apples (Annona squamosa), biscuit, chicory leaves (Cichorium intybus var. foliosum), and docks (Rumex). This could make bergaptol a potential biomarker for the consumption of these foods. Bergaptol is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Based on a literature review very few articles have been published on Bergaptol.
Structure
Data?1676999881
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013679 (Bergaptol)

Bergaptol
  Mrv1572001071617272D          

 15 17  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 O   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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6425    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1274    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6425   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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    0.8250    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  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
  2 15  2  0  0  0  0
  9 15  1  0  0  0  0
M  END
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3D MOL for HMDB0013679 (Bergaptol)

HMDB0013679
     RDKit          3D
Bergaptol
 21 23  0  0  0  0  0  0  0  0999 V2000
    4.4591    1.1047    0.4249 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2896    0.6147    0.3106 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1573   -0.7576    0.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8899   -1.2773    0.1548 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7942   -0.4435    0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4974   -0.9449   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6488   -2.3182   -0.0931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764   -0.0964   -0.1460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9305   -0.2821   -0.2728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5128    0.9613   -0.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5693    1.8497   -0.2088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3845    1.2732   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942    1.7408    0.0166 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0102    0.9186    0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404    1.4106    0.2259 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0531   -1.3878    0.3515 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7577   -2.3481    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5396   -2.7827   -0.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4071   -1.2509   -0.3306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5609    1.1882   -0.4010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0700    2.8277    0.0474 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
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15  2  1  0
 14  5  1  0
 12  8  2  0
  3 16  1  0
  4 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 13 21  1  0
M  END
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3D SDF for HMDB0013679 (Bergaptol)

Bergaptol
  Mrv1572001071617272D          

 15 17  0  0  0  0            999 V2000
    2.1434    2.0625    0.0000 O   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
    2.8579    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6425    1.0799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1274    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6425   -0.2549    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    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    0.8250    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  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  3  7  2  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 11 13  1  0  0  0  0
 13 14  2  0  0  0  0
 14 15  1  0  0  0  0
  2 15  2  0  0  0  0
  9 15  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013679

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C2C=CC(=O)OC2=CC2=C1C=CO2

> <INCHI_IDENTIFIER>
InChI=1S/C11H6O4/c12-10-2-1-6-9(15-10)5-8-7(11(6)13)3-4-14-8/h1-5,13H

> <INCHI_KEY>
GIJHDGJRTUSBJR-UHFFFAOYSA-N

> <FORMULA>
C11H6O4

> <MOLECULAR_WEIGHT>
202.165

> <EXACT_MASS>
202.026608673

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
21

> <JCHEM_AVERAGE_POLARIZABILITY>
18.937868719923827

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-hydroxy-7H-furo[3,2-g]chromen-7-one

> <ALOGPS_LOGP>
1.86

> <JCHEM_LOGP>
1.6389176943333332

> <ALOGPS_LOGS>
-2.36

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA_STRONGEST_ACIDIC>
6.4494231965733

> <JCHEM_PKA_STRONGEST_BASIC>
-2.83145388841103

> <JCHEM_POLAR_SURFACE_AREA>
59.67000000000001

> <JCHEM_REFRACTIVITY>
52.3706

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
8.88e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
bergaptol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0013679 (Bergaptol)

HMDB0013679
     RDKit          3D
Bergaptol
 21 23  0  0  0  0  0  0  0  0999 V2000
    4.4591    1.1047    0.4249 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2896    0.6147    0.3106 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1573   -0.7576    0.2785 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8899   -1.2773    0.1548 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7942   -0.4435    0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4974   -0.9449   -0.0593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6488   -2.3182   -0.0931 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5764   -0.0964   -0.1460 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9305   -0.2821   -0.2728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5128    0.9613   -0.3082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5693    1.8497   -0.2088 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3845    1.2732   -0.1085 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0942    1.7408    0.0166 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0102    0.9186    0.1060 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2404    1.4106    0.2259 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0531   -1.3878    0.3515 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7577   -2.3481    0.1271 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5396   -2.7827   -0.1815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4071   -1.2509   -0.3306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5609    1.1882   -0.4010 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.0700    2.8277    0.0474 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
  6  7  1  0
  6  8  1  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  2  0
 14 15  1  0
 15  2  1  0
 14  5  1  0
 12  8  2  0
  3 16  1  0
  4 17  1  0
  7 18  1  0
  9 19  1  0
 10 20  1  0
 13 21  1  0
M  END
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PDB for HMDB0013679 (Bergaptol)

HEADER    PROTEIN                                 07-JAN-16   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Bergaptol                                         
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   07-JAN-16         0                                  
HETATM    1  O   UNK     0       4.001   3.850   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       4.001   2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.335   1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       6.799   2.016   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       7.704   0.770   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.799  -0.476   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       5.335   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      -1.334  -0.770   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.000   1.540   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   15                                                  
CONECT    3    2    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    3    8                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   15                                                  
CONECT   10    9   11                                                       
CONECT   11   10   12   13                                                  
CONECT   12   11                                                            
CONECT   13   11   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14    2    9                                                  
MASTER        0    0    0    0    0    0    0    0   15    0   34    0
END
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3D PDB for HMDB0013679 (Bergaptol)

COMPND    HMDB0013679
HETATM    1  O1  UNL     1       4.459   1.105   0.425  1.00  0.00           O  
HETATM    2  C1  UNL     1       3.290   0.615   0.311  1.00  0.00           C  
HETATM    3  C2  UNL     1       3.157  -0.758   0.279  1.00  0.00           C  
HETATM    4  C3  UNL     1       1.890  -1.277   0.155  1.00  0.00           C  
HETATM    5  C4  UNL     1       0.794  -0.444   0.066  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.497  -0.945  -0.059  1.00  0.00           C  
HETATM    7  O2  UNL     1      -0.649  -2.318  -0.093  1.00  0.00           O  
HETATM    8  C6  UNL     1      -1.576  -0.096  -0.146  1.00  0.00           C  
HETATM    9  C7  UNL     1      -2.931  -0.282  -0.273  1.00  0.00           C  
HETATM   10  C8  UNL     1      -3.513   0.961  -0.308  1.00  0.00           C  
HETATM   11  O3  UNL     1      -2.569   1.850  -0.209  1.00  0.00           O  
HETATM   12  C9  UNL     1      -1.385   1.273  -0.108  1.00  0.00           C  
HETATM   13  C10 UNL     1      -0.094   1.741   0.017  1.00  0.00           C  
HETATM   14  C11 UNL     1       1.010   0.919   0.106  1.00  0.00           C  
HETATM   15  O4  UNL     1       2.240   1.411   0.226  1.00  0.00           O  
HETATM   16  H1  UNL     1       4.053  -1.388   0.352  1.00  0.00           H  
HETATM   17  H2  UNL     1       1.758  -2.348   0.127  1.00  0.00           H  
HETATM   18  H3  UNL     1      -1.540  -2.783  -0.182  1.00  0.00           H  
HETATM   19  H4  UNL     1      -3.407  -1.251  -0.331  1.00  0.00           H  
HETATM   20  H5  UNL     1      -4.561   1.188  -0.401  1.00  0.00           H  
HETATM   21  H6  UNL     1       0.070   2.828   0.047  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3   15
CONECT    3    4    4   16
CONECT    4    5   17
CONECT    5    6    6   14
CONECT    6    7    8
CONECT    7   18
CONECT    8    9   12   12
CONECT    9   10   10   19
CONECT   10   11   20
CONECT   11   12
CONECT   12   13
CONECT   13   14   14   21
CONECT   14   15
END
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SMILES for HMDB0013679 (Bergaptol)

OC1=C2C=CC(=O)OC2=CC2=C1C=CO2
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INCHI for HMDB0013679 (Bergaptol)

InChI=1S/C11H6O4/c12-10-2-1-6-9(15-10)5-8-7(11(6)13)3-4-14-8/h1-5,13H
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5-HydroxyfuranocoumarinChEBI
5-HydroxypsoralenChEBI
4-Hydroxy-7H-furo(3,2-g)chromen-7-oneMeSH
4-Hydroxy-7H-furo[3,2-g]chromen-7-oneHMDB
4-Hydroxy-7H-furo[3,2-g]chromen-7-one (acd/name 4.0)HMDB
5-HYDROXY-psoralinHMDB
BergaptolsHMDB
Chemical FormulaC11H6O4
Average Molecular Weight202.165
Monoisotopic Molecular Weight202.026608673
IUPAC Name4-hydroxy-7H-furo[3,2-g]chromen-7-one
Traditional Namebergaptol
CAS Registry Number486-60-2
SMILES
OC1=C2C=CC(=O)OC2=CC2=C1C=CO2
InChI Identifier
InChI=1S/C11H6O4/c12-10-2-1-6-9(15-10)5-8-7(11(6)13)3-4-14-8/h1-5,13H
InChI KeyGIJHDGJRTUSBJR-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 5-hydroxypsoralens. These are psoralens containing a hydroxyl group attached at the C5 position of the psoralen group.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassFuranocoumarins
Direct Parent5-hydroxypsoralens
Alternative Parents
Substituents
  • 5-hydroxypsoralen
  • Benzopyran
  • 1-benzopyran
  • Benzofuran
  • 1-hydroxy-4-unsubstituted benzenoid
  • Pyranone
  • Pyran
  • Benzenoid
  • Furan
  • Heteroaromatic compound
  • Lactone
  • Oxacycle
  • Organoheterocyclic compound
  • Organooxygen compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB002543
KNApSAcK IDC00000581
Chemspider ID4444066
KEGG Compound IDC00758
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkBergaptol
METLIN IDNot Available
PubChem Compound5280371
PDB IDNot Available
ChEBI ID17377
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Enzymes

Enzyme Details
1. UDP-glucuronosyltransferase 1-1
General function:
Involved in transferase activity, transferring hexosyl groups
Specific function:
UDPGT is of major importance in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This isoform glucuronidates bilirubin IX-alpha to form both the IX-alpha-C8 and IX-alpha-C12 monoconjugates and diconjugate. Is also able to catalyze the glucuronidation of 17beta-estradiol, 17alpha-ethinylestradiol, 1-hydroxypyrene, 4-methylumbelliferone, 1-naphthol, paranitrophenol, scopoletin, and umbelliferone.
Gene Name:
UGT1A1
Uniprot ID:
P22309
Molecular weight:
59590.91
Reactions
Bergaptol → 3,4,5-trihydroxy-6-({7-oxo-7H-furo[3,2-g]chromen-4-yl}oxy)oxane-2-carboxylic aciddetails