Showing metabocard for Protocatechuate (MMDBc0049961)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2022-04-29 22:47:09 UTC
Update Date2022-09-01 02:17:35 UTC
Metabolite IDMMDBc0049961
Metabolite Identification
Common NameProtocatechuate
DescriptionProtocatechuic acid, also known as protocatechuate or 3,4-dihydroxybenzoate, 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. The enzyme protocatechuate 3,4-dioxygenase uses 3,4-dihydroxybenzoate and O2 to produce 3-carboxy-cis,cis-muconate. Protocatechuic acid is a drug. In the analogous hardening of the cockroach ootheca, the phenolic substance concerned is protocatechuic acid. Protocatechuic acid is a mild, balsamic, and phenolic tasting compound. Outside of the human body, protocatechuic acid is found, on average, in the highest concentration in a few different foods, such as garden onions, cocoa powders, and star anises and in a lower concentration in lentils, liquors, and red raspberries. Protocatechuic acid has also been detected, but not quantified in several different foods, such as cloud ear fungus, american pokeweeds, common mushrooms, fruits, and feijoa. This could make protocatechuic acid a potential biomarker for the consumption of these foods. It is also found in Allium cepa (17,540 ppm). It is a major metabolite of antioxidant polyphenols found in green tea. Similarly, PCA was reported to increase proliferation and inhibit apoptosis of neural stem cells. In vitro testing documented antioxidant and anti-inflammatory activity of PCA, while liver protection in vivo was measured by chemical markers and histological assessment.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f1240c9e588>


  Mrv1652309272007452D          

 11 11  0  0  0  0            999 V2000
   -0.8703    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993    0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5848   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8703   -0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0137    0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0138   -0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5586    0.4126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  1  9  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f1240c9e588>

HMDB0001856
     RDKit          3D
Protocatechuic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2677   -0.6454   -0.8475 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4629    0.2249   -0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9356    1.5030   -0.1701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0424   -0.0901   -0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5607   -1.3525   -0.5494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7886   -1.6538   -0.3861 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6919   -0.7069    0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0398   -1.0414    0.2061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2025    0.5545    0.3237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0837    1.5150    0.7621 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1389    0.8540    0.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2685    1.6422    0.7910 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2299   -2.1289   -0.8958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1731   -2.6499   -0.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6957   -0.3426    0.5278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7685    2.4641    0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5374    1.8537    0.3743 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  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11  4  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
 10 16  1  0
 11 17  1  0
M  END
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3D SDF for #<Metabolite:0x00007f1240c9e588>


  Mrv1652309272007452D          

 11 11  0  0  0  0            999 V2000
   -0.8703    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5847    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993    0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2993   -0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5848   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8703   -0.4124    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0137    0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0138   -0.8249    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558    0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1558    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5586    0.4126    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  1  1  0  0  0  0
  1  9  1  0  0  0  0
  3  7  1  0  0  0  0
  4  8  1  0  0  0  0
  9 10  2  0  0  0  0
  9 11  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049961

> <DATABASE_NAME>
MIME

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

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

> <INCHI_KEY>
YQUVCSBJEUQKSH-UHFFFAOYSA-N

> <FORMULA>
C7H6O4

> <MOLECULAR_WEIGHT>
154.121

> <EXACT_MASS>
154.026608673

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
17

> <JCHEM_AVERAGE_POLARIZABILITY>
13.8515611568227

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3,4-dihydroxybenzoic acid

> <ALOGPS_LOGP>
1.32

> <JCHEM_LOGP>
1.0236980806666667

> <ALOGPS_LOGS>
-1.10

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.401748678864411

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.160229176821464

> <JCHEM_PKA_STRONGEST_BASIC>
-6.341303650784174

> <JCHEM_POLAR_SURFACE_AREA>
77.76

> <JCHEM_REFRACTIVITY>
37.275999999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.24e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3,4-dihydroxybenzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f1240c9e588>

HMDB0001856
     RDKit          3D
Protocatechuic acid
 17 17  0  0  0  0  0  0  0  0999 V2000
    3.2677   -0.6454   -0.8475 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4629    0.2249   -0.4490 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9356    1.5030   -0.1701 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0424   -0.0901   -0.2765 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5607   -1.3525   -0.5494 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7886   -1.6538   -0.3861 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6919   -0.7069    0.0526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0398   -1.0414    0.2061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2025    0.5545    0.3237 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0837    1.5150    0.7621 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1389    0.8540    0.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2685    1.6422    0.7910 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2299   -2.1289   -0.8958 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1731   -2.6499   -0.6005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6957   -0.3426    0.5278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7685    2.4641    0.9760 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5374    1.8537    0.3743 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  2  0
  7  8  1  0
  7  9  1  0
  9 10  1  0
  9 11  2  0
 11  4  1  0
  3 12  1  0
  5 13  1  0
  6 14  1  0
  8 15  1  0
 10 16  1  0
 11 17  1  0
M  END
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PDB for #<Metabolite:0x00007f1240c9e588>

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  C   UNK     0      -1.625   0.770   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -2.958   1.540   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.292   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -4.292  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.958  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.625  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0      -5.626   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -5.626  -1.540   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      -0.291   1.540   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      -0.291   3.080   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.043   0.770   0.000  0.00  0.00           O+0
CONECT    1    2    6    9                                                  
CONECT    2    1    3                                                       
CONECT    3    2    4    7                                                  
CONECT    4    3    5    8                                                  
CONECT    5    4    6                                                       
CONECT    6    5    1                                                       
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    1   10   11                                                  
CONECT   10    9                                                            
CONECT   11    9                                                            
MASTER        0    0    0    0    0    0    0    0   11    0   22    0
END
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3D PDB for #<Metabolite:0x00007f1240c9e588>

COMPND    HMDB0001856
HETATM    1  O1  UNL     1       3.268  -0.645  -0.847  1.00  0.00           O  
HETATM    2  C1  UNL     1       2.463   0.225  -0.449  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.936   1.503  -0.170  1.00  0.00           O  
HETATM    4  C2  UNL     1       1.042  -0.090  -0.277  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.561  -1.353  -0.549  1.00  0.00           C  
HETATM    6  C4  UNL     1      -0.789  -1.654  -0.386  1.00  0.00           C  
HETATM    7  C5  UNL     1      -1.692  -0.707   0.053  1.00  0.00           C  
HETATM    8  O3  UNL     1      -3.040  -1.041   0.206  1.00  0.00           O  
HETATM    9  C6  UNL     1      -1.203   0.555   0.324  1.00  0.00           C  
HETATM   10  O4  UNL     1      -2.084   1.515   0.762  1.00  0.00           O  
HETATM   11  C7  UNL     1       0.139   0.854   0.161  1.00  0.00           C  
HETATM   12  H1  UNL     1       3.268   1.642   0.791  1.00  0.00           H  
HETATM   13  H2  UNL     1       1.230  -2.129  -0.896  1.00  0.00           H  
HETATM   14  H3  UNL     1      -1.173  -2.650  -0.601  1.00  0.00           H  
HETATM   15  H4  UNL     1      -3.696  -0.343   0.528  1.00  0.00           H  
HETATM   16  H5  UNL     1      -1.769   2.464   0.976  1.00  0.00           H  
HETATM   17  H6  UNL     1       0.537   1.854   0.374  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   12
CONECT    4    5    5   11
CONECT    5    6   13
CONECT    6    7    7   14
CONECT    7    8    9
CONECT    8   15
CONECT    9   10   11   11
CONECT   10   16
CONECT   11   17
END
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SMILES for #<Metabolite:0x00007f1240c9e588>

OC(=O)C1=CC(O)=C(O)C=C1
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INCHI for #<Metabolite:0x00007f1240c9e588>

InChI=1S/C7H6O4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H,(H,10,11)
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Synonyms
ValueSource
4,5-Dihydroxybenzoic acidChEBI
4-Carboxy-1,2-dihydroxybenzeneChEBI
Protocatehuic acidChEBI
3,4-Dihydroxybenzoic acidKegg
ProtocatechuateKegg
4,5-DihydroxybenzoateGenerator
ProtocatehuateGenerator
3,4-DihydroxybenzoateGenerator
Protocatechuic acid, monosodium saltHMDB
Protocatechuic acid, carboxy-14C-labeledHMDB
2,4-DihydroxybenzoateHMDB
2,4-Dihydroxybenzoic acidHMDB
b-ResorcylateHMDB
b-Resorcylic acidHMDB
beta-ResorcylateHMDB
beta-Resorcylic acidHMDB
3,4-DHBAHMDB
1,2-Dihydroxybenzene-4-carboxylic acidPhytoBank
Protocatechoic acidPhytoBank
Proto-catechuic acidPhytoBank
Protocatechuic acidHMDB
Molecular FormulaC7H6O4
Average Mass154.121
Monoisotopic Mass154.026608673
IUPAC Name3,4-dihydroxybenzoic acid
Traditional Name3,4-dihydroxybenzoic acid
CAS Registry NumberNot Available
SMILES
OC(=O)C1=CC(O)=C(O)C=C1
InChI Identifier
InChI=1S/C7H6O4/c8-5-2-1-4(7(10)11)3-6(5)9/h1-3,8-9H,(H,10,11)
InChI KeyYQUVCSBJEUQKSH-UHFFFAOYSA-N