Showing metabocard for Gentisic acid (MMDBc0000336)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-12-10 18:35:37 UTC
Update Date2024-10-15 20:52:01 UTC
Metabolite IDMMDBc0000336
Metabolite Identification
Common NameGentisic acid
DescriptionGentisic acid, also known as gentisate or 2,5-dioxybenzoate, belongs to the class of organic compounds known as hydroxybenzoic acid derivatives. Hydroxybenzoic acid derivatives are compounds containing a hydroxybenzoic acid (or a derivative), which is a benzene ring bearing a carboxyl and a hydroxyl groups. Gentisic acid is also classified as a dihydroxybenzoic acid. It is a derivative of benzoic acid and a minor (1%) product of the metabolic break down of aspirin, which is excreted by the kidneys. Gentisic acid is found in essentially all organisms ranging from bacteria to fungi to plants to animals. Gentisic acid has been associated with a number of useful effects on human health and exhibits anti-inflammatory, antigenotoxic, hepatoprotective, neuroprotective, antimicrobial, and especially antioxidant activities (PMID: 31825145 ). It is widely distributed in plants as a secondary plant product such as Gentiana spp., Citrus spp., Vitis vinifera, Pterocarpus santalinus, Helianthus tuberosus, Hibiscus rosa-sinensis, Olea europaea, and Sesamum indicum and in fruits such as avocados, batoko plum, kiwi fruits, apple, bitter melon, black berries, pears, and some mushrooms (PMID: 31825145 ). Gentisic acid is found in higher concentrations in a number of foods such as tarragons, common thymes, and common sages and in a lower concentration in grape wines, rosemaries, and sweet marjorams. Gentisic acid has also been shown to act as a pathogen-inducible signal for the activation of plant defenses in tomato plants and cucumbers (PMID: 16321412 ; https://doi.org/10.1094/MPMI.1999.12.3.227).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f92345f6bd0>

Gentisic acid
  Mrv1652309032023542D          

 11 11  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   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
    1.4289    2.4750    0.0000 O   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
    2.1434    1.2375    0.0000 O   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 C   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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  4 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f92345f6bd0>

HMDB0000152
     RDKit          3D
Gentisic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6682    1.3941   -0.1686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4366    1.6222   -0.1752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9122    2.8905   -0.2711 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5028    0.5047   -0.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8639    0.6917   -0.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7080   -0.3877    0.0137 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0957   -0.1994    0.0117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2557   -1.6913    0.1131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -1.8648    0.1141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9783   -0.7973    0.0212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3573   -0.9558    0.0210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3779    3.6400    0.2256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2290    1.7171   -0.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4879    0.7448   -0.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9215   -2.5408    0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5043   -2.8689    0.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7126   -1.8992    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  4  1  0
  3 12  1  0
  5 13  1  0
  7 14  1  0
  8 15  1  0
  9 16  1  0
 11 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007f92345f6bd0>

Gentisic acid
  Mrv1652309032023542D          

 11 11  0  0  0  0            999 V2000
    0.0000    2.4750    0.0000 O   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
    1.4289    2.4750    0.0000 O   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
    2.1434    1.2375    0.0000 O   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 C   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
  1  2  1  0  0  0  0
  2  3  2  0  0  0  0
  2  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  7  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  2  0  0  0  0
  4 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000336

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)C1=C(O)C=CC(O)=C1

> <INCHI_IDENTIFIER>
InChI=1S/C7H6O4/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3,8-9H,(H,10,11)

> <INCHI_KEY>
WXTMDXOMEHJXQO-UHFFFAOYSA-N

> <FORMULA>
C7H6O4

> <MOLECULAR_WEIGHT>
154.121

> <EXACT_MASS>
154.026608673

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.777778121056386

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2,5-dihydroxybenzoic acid

> <ALOGPS_LOGP>
1.23

> <JCHEM_LOGP>
1.6736980806666664

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
10.024335409652737

> <JCHEM_PKA_STRONGEST_ACIDIC>
2.5281776702814094

> <JCHEM_PKA_STRONGEST_BASIC>
-5.934430569892133

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
37.276

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2,5-dihydroxybenzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f92345f6bd0>

HMDB0000152
     RDKit          3D
Gentisic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
   -2.6682    1.3941   -0.1686 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4366    1.6222   -0.1752 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9122    2.8905   -0.2711 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5028    0.5047   -0.0778 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8639    0.6917   -0.0799 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7080   -0.3877    0.0137 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0957   -0.1994    0.0117 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2557   -1.6913    0.1131 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1114   -1.8648    0.1141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9783   -0.7973    0.0212 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3573   -0.9558    0.0210 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3779    3.6400    0.2256 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2290    1.7171   -0.1579 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4879    0.7448   -0.0596 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9215   -2.5408    0.1868 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5043   -2.8689    0.1902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7126   -1.8992    0.0926 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  1  0
  6  8  2  0
  8  9  1  0
  9 10  2  0
 10 11  1  0
 10  4  1  0
  3 12  1  0
  5 13  1  0
  7 14  1  0
  8 15  1  0
  9 16  1  0
 11 17  1  0
M  END
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PDB for #<Metabolite:0x00007f92345f6bd0>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Gentisic acid                                     
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  O   UNK     0       0.000   4.620   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   3.850   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       2.667   4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0       1.334   2.310   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       2.667   1.540   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       0.000   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   1.540   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5   11                                                  
CONECT    5    4    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00007f92345f6bd0>

COMPND    HMDB0000152
HETATM    1  O1  UNL     1      -2.668   1.394  -0.169  1.00  0.00           O  
HETATM    2  C1  UNL     1      -1.437   1.622  -0.175  1.00  0.00           C  
HETATM    3  O2  UNL     1      -0.912   2.890  -0.271  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.503   0.505  -0.078  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.864   0.692  -0.080  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.708  -0.388   0.014  1.00  0.00           C  
HETATM    7  O3  UNL     1       3.096  -0.199   0.012  1.00  0.00           O  
HETATM    8  C5  UNL     1       1.256  -1.691   0.113  1.00  0.00           C  
HETATM    9  C6  UNL     1      -0.111  -1.865   0.114  1.00  0.00           C  
HETATM   10  C7  UNL     1      -0.978  -0.797   0.021  1.00  0.00           C  
HETATM   11  O4  UNL     1      -2.357  -0.956   0.021  1.00  0.00           O  
HETATM   12  H1  UNL     1      -1.378   3.640   0.226  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.229   1.717  -0.158  1.00  0.00           H  
HETATM   14  H3  UNL     1       3.488   0.745  -0.060  1.00  0.00           H  
HETATM   15  H4  UNL     1       1.921  -2.541   0.187  1.00  0.00           H  
HETATM   16  H5  UNL     1      -0.504  -2.869   0.190  1.00  0.00           H  
HETATM   17  H6  UNL     1      -2.713  -1.899   0.093  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    5   10
CONECT    5    6   13
CONECT    6    7    8    8
CONECT    7   14
CONECT    8    9   15
CONECT    9   10   10   16
CONECT   10   11
CONECT   11   17
END
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SMILES for #<Metabolite:0x00007f92345f6bd0>

OC(=O)C1=C(O)C=CC(O)=C1
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INCHI for #<Metabolite:0x00007f92345f6bd0>

InChI=1S/C7H6O4/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3,8-9H,(H,10,11)
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Synonyms
ValueSource
2,5-DihydroxybenzoateChEBI
5-Hydroxysalicylic acidChEBI
GentisateChEBI
Hydroquinonecarboxylic acidChEBI
2,5-Dihydroxybenzoic acidKegg
5-HydroxysalicylateGenerator
HydroquinonecarboxylateGenerator
2,5-DioxybenzoateHMDB
2,5-Dioxybenzoic acidHMDB
3,6-DihydroxybenzoateHMDB
3,6-Dihydroxybenzoic acidHMDB
5-Hydroxy-salicylateHMDB
5-Hydroxy-salicylic acidHMDB
CarboxyhydroquinoneHMDB
DihydroxybenzoicacidHMDB
GensigenHMDB
GensigonHMDB
GentisinateHMDB
Gentisinic acidHMDB
2,5-Dihydroxybenzoic acid, monosodium saltHMDB
Lithium 2,5-dihydroxybenzoateHMDB
Gentisic acidChEBI
Hydroquinone carboxylic acidHMDB
Molecular FormulaC7H6O4
Average Mass154.121
Monoisotopic Mass154.026608673
IUPAC Name2,5-dihydroxybenzoic acid
Traditional Name2,5-dihydroxybenzoic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=C(O)C=CC(O)=C1
InChI Identifier
InChI=1S/C7H6O4/c8-4-1-2-6(9)5(3-4)7(10)11/h1-3,8-9H,(H,10,11)
InChI KeyWXTMDXOMEHJXQO-UHFFFAOYSA-N