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Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2012-09-11 17:45:17 UTC

Update Date

2022-03-07 02:53:06 UTC

HMDB ID

HMDB0031760

Secondary Accession Numbers

HMDB31760

Metabolite Identification

Common Name

Gentisin

Description

Gentisin, also known as gentianin or gentianic acid, belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring. Gentisin is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review a significant number of articles have been published on Gentisin.

Structure

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

HMDB0031760
     RDKit          3D
Gentisin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.2054   -0.6686   -0.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0060   -1.3570   -0.5626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7776   -0.7650   -0.3035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7174    0.4758    0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5210    1.0975    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4468    2.3498    1.1962 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    0.4320    0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8393    1.0474    0.4937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8925    2.1607    1.0409 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0100    0.3882    0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2352    0.9497    0.3819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3835    0.2777    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6545    0.8187    0.2530 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2931   -0.9597   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0480   -1.5019   -0.8214 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8658   -0.8449   -0.4662 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063   -1.3891   -0.7035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4226   -0.8022   -0.3843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239   -1.4303   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1789    0.3274   -0.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0986   -1.2407   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1046   -0.4285    0.8885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6314    1.0156    0.5967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3154    2.8041    1.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2854    1.9268    0.8621 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6985    1.7313    0.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1596   -1.5196   -0.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9842   -2.4854   -1.3044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -2.4101   -1.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19  3  1  0
 18  7  1  0
 16 10  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
 11 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 19 29  1  0
M  END


  Mrv1652309272007402D          

 19 21  0  0  0  0            999 V2000
 9998.4172 9997.5506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9995.5576 9998.3755    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9999.8457 9997.5506    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.274810000.0254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
10001.9883 9999.6129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.845610000.0254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.8456 9998.3755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.5600 9998.7879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
10000.5600 9999.6129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.987110000.0253    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.2726 9999.6128    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.2726 9998.7880    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9996.9869 9998.3755    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.416710000.0254    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
 9997.7023 9999.6129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9997.7023 9998.7879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9998.4167 9998.3756    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.1311 9998.7879    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
 9999.1311 9999.6129    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  1  0  0  0  0
  7  8  1  0  0  0  0
  8  9  2  0  0  0  0
  9  6  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
  9  4  1  0  0  0  0
  7  3  1  0  0  0  0
 12  2  1  0  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  1  0  0  0  0
 14 15  1  0  0  0  0
 14 19  1  0  0  0  0
  1 17  2  0  0  0  0
  6 19  2  0  0  0  0
 18  7  2  0  0  0  0
 15 10  2  0  0  0  0
 13 16  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031760

> <DATABASE_NAME>
hmdb

> <SMILES>
COC1=CC(O)=C2C(=O)C3=CC(O)=CC=C3OC2=C1

> <INCHI_IDENTIFIER>
InChI=1S/C14H10O5/c1-18-8-5-10(16)13-12(6-8)19-11-3-2-7(15)4-9(11)14(13)17/h2-6,15-16H,1H3

> <INCHI_KEY>
XOXYHGOIRWABTC-UHFFFAOYSA-N

> <FORMULA>
C14H10O5

> <MOLECULAR_WEIGHT>
258.2262

> <EXACT_MASS>
258.05282343

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
29

> <JCHEM_AVERAGE_POLARIZABILITY>
25.382698467297793

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
1,7-dihydroxy-3-methoxy-9H-xanthen-9-one

> <ALOGPS_LOGP>
2.80

> <JCHEM_LOGP>
2.844838311333333

> <ALOGPS_LOGS>
-3.05

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
9.180837760162778

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.263553267404538

> <JCHEM_PKA_STRONGEST_BASIC>
-3.726859351280583

> <JCHEM_POLAR_SURFACE_AREA>
75.99000000000001

> <JCHEM_REFRACTIVITY>
67.24130000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.29e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
gentisin

> <JCHEM_VEBER_RULE>
0

$$$$

HMDB0031760
     RDKit          3D
Gentisin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.2054   -0.6686   -0.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0060   -1.3570   -0.5626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7776   -0.7650   -0.3035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7174    0.4758    0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5210    1.0975    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4468    2.3498    1.1962 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    0.4320    0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8393    1.0474    0.4937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8925    2.1607    1.0409 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0100    0.3882    0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2352    0.9497    0.3819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3835    0.2777    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6545    0.8187    0.2530 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2931   -0.9597   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0480   -1.5019   -0.8214 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8658   -0.8449   -0.4662 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063   -1.3891   -0.7035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4226   -0.8022   -0.3843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239   -1.4303   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1789    0.3274   -0.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0986   -1.2407   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1046   -0.4285    0.8885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6314    1.0156    0.5967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3154    2.8041    1.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2854    1.9268    0.8621 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6985    1.7313    0.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1596   -1.5196   -0.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9842   -2.4854   -1.3044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -2.4101   -1.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19  3  1  0
 18  7  1  0
 16 10  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
 11 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 19 29  1  0
M  END

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  O   UNK     0    8663.7128662.094   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0    8658.3748663.634   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0    8666.3798662.094   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0    8669.0468666.714   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0    8670.3788665.944   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0    8666.3788666.714   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0    8666.3788663.634   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0    8667.7128664.404   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0    8667.7128665.944   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0    8661.0438666.714   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0    8659.7098665.944   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0    8659.7098664.404   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0    8661.0428663.634   0.000  0.00  0.00           C+0
HETATM   14  O   UNK     0    8663.7118666.714   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0    8662.3788665.944   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0    8662.3788664.404   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0    8663.7118663.634   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0    8665.0458664.404   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0    8665.0458665.944   0.000  0.00  0.00           C+0
CONECT    1   17                                                            
CONECT    2   12                                                            
CONECT    3    7                                                            
CONECT    4    5    9                                                       
CONECT    5    4                                                            
CONECT    6    9   19                                                       
CONECT    7    8    3   18                                                  
CONECT    8    7    9                                                       
CONECT    9    8    6    4                                                  
CONECT   10   11   15                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13    2                                                  
CONECT   13   12   16                                                       
CONECT   14   15   19                                                       
CONECT   15   16   14   10                                                  
CONECT   16   15   17   13                                                  
CONECT   17   16   18    1                                                  
CONECT   18   17   19    7                                                  
CONECT   19   18   14    6                                                  
MASTER        0    0    0    0    0    0    0    0   19    0   42    0
END

COMPND    HMDB0031760
HETATM    1  C1  UNL     1      -5.205  -0.669  -0.191  1.00  0.00           C  
HETATM    2  O1  UNL     1      -4.006  -1.357  -0.563  1.00  0.00           O  
HETATM    3  C2  UNL     1      -2.778  -0.765  -0.303  1.00  0.00           C  
HETATM    4  C3  UNL     1      -2.717   0.476   0.306  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.521   1.098   0.581  1.00  0.00           C  
HETATM    6  O2  UNL     1      -1.447   2.350   1.196  1.00  0.00           O  
HETATM    7  C5  UNL     1      -0.357   0.432   0.222  1.00  0.00           C  
HETATM    8  C6  UNL     1       0.839   1.047   0.494  1.00  0.00           C  
HETATM    9  O3  UNL     1       0.892   2.161   1.041  1.00  0.00           O  
HETATM   10  C7  UNL     1       2.010   0.388   0.138  1.00  0.00           C  
HETATM   11  C8  UNL     1       3.235   0.950   0.382  1.00  0.00           C  
HETATM   12  C9  UNL     1       4.383   0.278   0.020  1.00  0.00           C  
HETATM   13  O4  UNL     1       5.654   0.819   0.253  1.00  0.00           O  
HETATM   14  C10 UNL     1       4.293  -0.960  -0.587  1.00  0.00           C  
HETATM   15  C11 UNL     1       3.048  -1.502  -0.821  1.00  0.00           C  
HETATM   16  C12 UNL     1       1.866  -0.845  -0.466  1.00  0.00           C  
HETATM   17  O5  UNL     1       0.706  -1.389  -0.704  1.00  0.00           O  
HETATM   18  C13 UNL     1      -0.423  -0.802  -0.384  1.00  0.00           C  
HETATM   19  C14 UNL     1      -1.624  -1.430  -0.662  1.00  0.00           C  
HETATM   20  H1  UNL     1      -5.179   0.327  -0.719  1.00  0.00           H  
HETATM   21  H2  UNL     1      -6.099  -1.241  -0.437  1.00  0.00           H  
HETATM   22  H3  UNL     1      -5.105  -0.429   0.889  1.00  0.00           H  
HETATM   23  H4  UNL     1      -3.631   1.016   0.597  1.00  0.00           H  
HETATM   24  H5  UNL     1      -2.315   2.804   1.443  1.00  0.00           H  
HETATM   25  H6  UNL     1       3.285   1.927   0.862  1.00  0.00           H  
HETATM   26  H7  UNL     1       5.699   1.731   0.702  1.00  0.00           H  
HETATM   27  H8  UNL     1       5.160  -1.520  -0.886  1.00  0.00           H  
HETATM   28  H9  UNL     1       2.984  -2.485  -1.304  1.00  0.00           H  
HETATM   29  H10 UNL     1      -1.650  -2.410  -1.144  1.00  0.00           H  
CONECT    1    2   20   21   22
CONECT    2    3
CONECT    3    4    4   19
CONECT    4    5   23
CONECT    5    6    7    7
CONECT    6   24
CONECT    7    8   18
CONECT    8    9    9   10
CONECT   10   11   11   16
CONECT   11   12   25
CONECT   12   13   14   14
CONECT   13   26
CONECT   14   15   27
CONECT   15   16   16   28
CONECT   16   17
CONECT   17   18
CONECT   18   19   19
CONECT   19   29
END

HMDB0031760
     RDKit          3D
Gentisin
 29 31  0  0  0  0  0  0  0  0999 V2000
   -5.2054   -0.6686   -0.1915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0060   -1.3570   -0.5626 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7776   -0.7650   -0.3035 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7174    0.4758    0.3064 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5210    1.0975    0.5811 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4468    2.3498    1.1962 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3567    0.4320    0.2222 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8393    1.0474    0.4937 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8925    2.1607    1.0409 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0100    0.3882    0.1377 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2352    0.9497    0.3819 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3835    0.2777    0.0202 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6545    0.8187    0.2530 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2931   -0.9597   -0.5872 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0480   -1.5019   -0.8214 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8658   -0.8449   -0.4662 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7063   -1.3891   -0.7035 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4226   -0.8022   -0.3843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6239   -1.4303   -0.6620 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1789    0.3274   -0.7194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0986   -1.2407   -0.4374 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1046   -0.4285    0.8885 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6314    1.0156    0.5967 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3154    2.8041    1.4432 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2854    1.9268    0.8621 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6985    1.7313    0.7016 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1596   -1.5196   -0.8862 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9842   -2.4854   -1.3044 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6498   -2.4101   -1.1441 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  2  0
  4  5  1  0
  5  6  1  0
  5  7  2  0
  7  8  1  0
  8  9  2  0
  8 10  1  0
 10 11  2  0
 11 12  1  0
 12 13  1  0
 12 14  2  0
 14 15  1  0
 15 16  2  0
 16 17  1  0
 17 18  1  0
 18 19  2  0
 19  3  1  0
 18  7  1  0
 16 10  1  0
  1 20  1  0
  1 21  1  0
  1 22  1  0
  4 23  1  0
  6 24  1  0
 11 25  1  0
 13 26  1  0
 14 27  1  0
 15 28  1  0
 19 29  1  0
M  END

View in JSmol View Stereo Labels

Synonyms

Value	Source
1,7-Dihydroxy-3-methoxyxanthone	ChEBI
1,7-Dihydroxy-3-methoxy-9H-xanthen-9-one	HMDB
1,7-Dihydroxy-3-methoxy-xanthen-9-one	HMDB
1,7-Dihydroxy-3-methoxyxanthen-9-one	HMDB
Gentianic acid	HMDB
Gentianin	HMDB
Gentianin?	HMDB
Gentisine	HMDB

Chemical Formula

C₁₄H₁₀O₅

Average Molecular Weight

258.2262

Monoisotopic Molecular Weight

258.05282343

IUPAC Name

1,7-dihydroxy-3-methoxy-9H-xanthen-9-one

Traditional Name

gentisin

CAS Registry Number

437-50-3

SMILES

COC1=CC(O)=C2C(=O)C3=CC(O)=CC=C3OC2=C1

InChI Identifier

InChI=1S/C14H10O5/c1-18-8-5-10(16)13-12(6-8)19-11-3-2-7(15)4-9(11)14(13)17/h2-6,15-16H,1H3

InChI Key

XOXYHGOIRWABTC-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as xanthones. These are polycyclic aromatic compounds containing a xanthene moiety conjugated to a ketone group at carbon 9. Xanthene is a tricyclic compound made up of two benzene rings linearly fused to each other through a pyran ring.

Kingdom

Organic compounds

Super Class

Organoheterocyclic compounds

Class

Benzopyrans

Sub Class

1-benzopyrans

Direct Parent

Xanthones

Alternative Parents

Substituents

Xanthone
Chromone
Anisole
1-hydroxy-4-unsubstituted benzenoid
1-hydroxy-2-unsubstituted benzenoid
Alkyl aryl ether
Pyranone
Benzenoid
Pyran
Heteroaromatic compound
Vinylogous acid
Ether
Oxacycle
Organic oxygen compound
Hydrocarbon derivative
Organooxygen compound
Organic oxide
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

aromatic ether (CHEBI:5324 )
polyphenol (CHEBI:5324 )
xanthones (CHEBI:5324 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Membrane (HMDB: HMDB0031760)
Cell membrane (HMDB: HMDB0031760)

Route of exposure

Enteral

Ingestion (HMDB: HMDB0031760)

Source

Endogenous

Endogenous (HMDB: HMDB0031760)

Plant

Plant (HMDB: HMDB0031760)

Exogenous

Food

Food (HMDB: HMDB0031760)

Herb and spice

Herbs and Spices (FooDB: FOOD00866)

Vegetable

Root vegetable

Root vegetables (FooDB: FOOD00873)

Beverage

Alcoholic beverage

Alcoholic beverages (FooDB: FOOD00854)

Exogenous (HMDB: HMDB0031760)

Process

Not Available

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	273 - 275 °C	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.3 mg/mL at 16 °C	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular Properties

Property	Value	Source
Water Solubility	0.23 g/L	ALOGPS
logP	2.8	ALOGPS
logP	2.84	ChemAxon
logS	-3	ALOGPS
pKa (Strongest Acidic)	8.26	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	75.99 Å²	ChemAxon
Rotatable Bond Count	1	ChemAxon
Refractivity	67.24 m³·mol⁻¹	ChemAxon
Polarizability	25.38 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	No	ChemAxon

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	159.969	31661259
DarkChem	[M-H]-	161.588	31661259
DeepCCS	[M+H]+	161.956	30932474
DeepCCS	[M-H]-	159.598	30932474
DeepCCS	[M-2H]-	192.484	30932474
DeepCCS	[M+Na]+	168.049	30932474
AllCCS	[M+H]+	156.9	32859911
AllCCS	[M+H-H2O]+	153.0	32859911
AllCCS	[M+NH4]+	160.6	32859911
AllCCS	[M+Na]+	161.7	32859911
AllCCS	[M-H]-	158.9	32859911
AllCCS	[M+Na-2H]-	158.2	32859911
AllCCS	[M+HCOO]-	157.6	32859911

Predicted Retention Times

Underivatized

Chromatographic Method	Retention Time	Reference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.	6.11 minutes	32390414
Predicted by Siyang on May 30, 2022	11.8433 minutes	33406817
Predicted by Siyang using ReTip algorithm on June 8, 2022	0.82 minutes	32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid	1958.2 seconds	40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid	324.2 seconds	40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid	146.2 seconds	40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid	191.1 seconds	40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	390.6 seconds	40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid	494.1 seconds	40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid	570.4 seconds	40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)	118.2 seconds	40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid	954.8 seconds	40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid	383.5 seconds	40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid	1388.6 seconds	40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	348.7 seconds	40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid	352.7 seconds	40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate	427.9 seconds	40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA	226.6 seconds	40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water	101.1 seconds	40023050

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Gentisin	COC1=CC(O)=C2C(=O)C3=CC(O)=CC=C3OC2=C1	4044.4	Standard polar	33892256
Gentisin	COC1=CC(O)=C2C(=O)C3=CC(O)=CC=C3OC2=C1	2604.7	Standard non polar	33892256
Gentisin	COC1=CC(O)=C2C(=O)C3=CC(O)=CC=C3OC2=C1	2639.4	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Gentisin,1TMS,isomer #1	COC1=CC(O[Si](C)(C)C)=C2C(=O)C3=CC(O)=CC=C3OC2=C1	2768.8	Semi standard non polar	33892256
Gentisin,1TMS,isomer #2	COC1=CC(O)=C2C(=O)C3=CC(O[Si](C)(C)C)=CC=C3OC2=C1	2821.9	Semi standard non polar	33892256
Gentisin,2TMS,isomer #1	COC1=CC(O[Si](C)(C)C)=C2C(=O)C3=CC(O[Si](C)(C)C)=CC=C3OC2=C1	2869.3	Semi standard non polar	33892256
Gentisin,1TBDMS,isomer #1	COC1=CC(O[Si](C)(C)C(C)(C)C)=C2C(=O)C3=CC(O)=CC=C3OC2=C1	3011.3	Semi standard non polar	33892256
Gentisin,1TBDMS,isomer #2	COC1=CC(O)=C2C(=O)C3=CC(O[Si](C)(C)C(C)(C)C)=CC=C3OC2=C1	3022.7	Semi standard non polar	33892256
Gentisin,2TBDMS,isomer #1	COC1=CC(O[Si](C)(C)C(C)(C)C)=C2C(=O)C3=CC(O[Si](C)(C)C(C)(C)C)=CC=C3OC2=C1	3289.2	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 - Gentisin GC-MS (Non-derivatized) - 70eV, Positive	splash10-0kcr-0690000000-2bbf6cbd52cc6e2f6015	2017-09-01	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gentisin GC-MS (2 TMS) - 70eV, Positive	splash10-00bi-4329000000-fdce50a515c2c215c906	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gentisin GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Gentisin 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 - Gentisin 10V, Positive-QTOF	splash10-0a4i-0090000000-f5fd12a26902f2c21dc7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 20V, Positive-QTOF	splash10-0a4i-0090000000-f5fd12a26902f2c21dc7	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 40V, Positive-QTOF	splash10-0a6r-3890000000-1c8202ff47295eb82fdc	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 10V, Negative-QTOF	splash10-0a4i-0090000000-6f3295d8b42fbe6db70c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 20V, Negative-QTOF	splash10-0a4i-0090000000-de58987fb8ac7f96cf51	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 40V, Negative-QTOF	splash10-0ar0-2590000000-d340c5bb7527d832db6c	2016-08-03	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 10V, Negative-QTOF	splash10-0a4i-0090000000-5c99e00473c8f7c5ab03	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 20V, Negative-QTOF	splash10-0a4i-0090000000-5c99e00473c8f7c5ab03	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 40V, Negative-QTOF	splash10-0ue9-1950000000-b9181e023acf15e1a719	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 10V, Positive-QTOF	splash10-0a4i-0090000000-adb7dbccff647a617461	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 20V, Positive-QTOF	splash10-0a4i-0090000000-adb7dbccff647a617461	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Gentisin 40V, Positive-QTOF	splash10-0pea-2490000000-75d431da9d2be7bedfca	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

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5281636

PDB ID

Not Available

ChEBI ID

5324

Food Biomarker Ontology

Not Available

VMH ID

Not Available

MarkerDB ID

Not Available

Good Scents ID

rw1827761

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

(). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Showing metabocard for Gentisin (HMDB0031760)

MOL for HMDB0031760 (Gentisin)

3D MOL for HMDB0031760 (Gentisin)

3D SDF for HMDB0031760 (Gentisin)

3D-SDF for HMDB0031760 (Gentisin)

PDB for HMDB0031760 (Gentisin)

3D PDB for HMDB0031760 (Gentisin)

SMILES for HMDB0031760 (Gentisin)

INCHI for HMDB0031760 (Gentisin)

Structure for HMDB0031760 (Gentisin)

3D Structure for HMDB0031760 (Gentisin)

Predicted Collision Cross Sections

Predicted Retention Times

Underivatized

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra