Showing NP-Card for Protocatechuic acid (NP0000497)

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Record Information
Version2.0
Created at2006-02-21 08:21:58 UTC
Updated at2025-02-11 15:48:56 UTC
NP-MRD IDNP0000497
Natural Product DOIhttps://doi.org/10.57994/0817
Secondary Accession NumbersNone
Natural Product Identification
Common NameProtocatechuic acid
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
Data?1628564079
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for NP0000497 (Protocatechuic acid)

  Mrv1652306202100163D          

 17 17  0  0  0  0            999 V2000
   -0.6271    0.8936    2.4910 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0048    0.0666    1.8597 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3771   -1.1015    2.4099 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4437    0.2090    0.4508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1721   -0.7964   -0.2060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5665   -0.6222   -1.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    0.5521   -2.1925 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6163    0.7206   -3.4908 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5077    1.5532   -1.5465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2124    2.6831   -2.2582 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1093    1.3925   -0.2251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0260   -1.0582    3.3241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4368   -1.7176    0.3078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1299   -1.3942   -2.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2744    1.6030   -3.7384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2901    3.2860   -1.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4542    2.1665    0.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9 11  2  0  0  0  0
  9 10  1  0  0  0  0
  4  2  1  0  0  0  0
 11  4  1  0  0  0  0
  2  3  1  0  0  0  0
  7  9  1  0  0  0  0
  2  1  2  0  0  0  0
  6 14  1  0  0  0  0
 11 17  1  0  0  0  0
  5 13  1  0  0  0  0
  8 15  1  0  0  0  0
 10 16  1  0  0  0  0
  3 12  1  0  0  0  0
M  END
Download

3D MOL for NP0000497 (Protocatechuic acid)

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
Download

3D SDF for NP0000497 (Protocatechuic acid)

  Mrv1652306202100163D          

 17 17  0  0  0  0            999 V2000
   -0.6271    0.8936    2.4910 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0048    0.0666    1.8597 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3771   -1.1015    2.4099 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4437    0.2090    0.4508 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1721   -0.7964   -0.2060 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5665   -0.6222   -1.5348 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2300    0.5521   -2.1925 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6163    0.7206   -3.4908 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5077    1.5532   -1.5465 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2124    2.6831   -2.2582 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1093    1.3925   -0.2251 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0260   -1.0582    3.3241 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4368   -1.7176    0.3078 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1299   -1.3942   -2.0506 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2744    1.6030   -3.7384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2901    3.2860   -1.6823 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4542    2.1665    0.2883 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  7  8  1  0  0  0  0
  9 11  2  0  0  0  0
  9 10  1  0  0  0  0
  4  2  1  0  0  0  0
 11  4  1  0  0  0  0
  2  3  1  0  0  0  0
  7  9  1  0  0  0  0
  2  1  2  0  0  0  0
  6 14  1  0  0  0  0
 11 17  1  0  0  0  0
  5 13  1  0  0  0  0
  8 15  1  0  0  0  0
 10 16  1  0  0  0  0
  3 12  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0000497

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC(=O)C1=C([H])C([H])=C(O[H])C(O[H])=C1[H]

> <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

$$$$
Download

3D-SDF for NP0000497 (Protocatechuic acid)

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
Download

PDB for NP0000497 (Protocatechuic acid)

HEADER    PROTEIN                                 20-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-JUN-21         0                                  
HETATM    1  O   UNK     0      -0.627   0.894   2.491  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.005   0.067   1.860  0.00  0.00           C+0
HETATM    3  O   UNK     0       0.377  -1.101   2.410  0.00  0.00           O+0
HETATM    4  C   UNK     0       0.444   0.209   0.451  0.00  0.00           C+0
HETATM    5  C   UNK     0       1.172  -0.796  -0.206  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.567  -0.622  -1.535  0.00  0.00           C+0
HETATM    7  C   UNK     0       1.230   0.552  -2.192  0.00  0.00           C+0
HETATM    8  O   UNK     0       1.616   0.721  -3.491  0.00  0.00           O+0
HETATM    9  C   UNK     0       0.508   1.553  -1.547  0.00  0.00           C+0
HETATM   10  O   UNK     0       0.212   2.683  -2.258  0.00  0.00           O+0
HETATM   11  C   UNK     0       0.109   1.393  -0.225  0.00  0.00           C+0
HETATM   12  H   UNK     0       0.026  -1.058   3.324  0.00  0.00           H+0
HETATM   13  H   UNK     0       1.437  -1.718   0.308  0.00  0.00           H+0
HETATM   14  H   UNK     0       2.130  -1.394  -2.051  0.00  0.00           H+0
HETATM   15  H   UNK     0       1.274   1.603  -3.738  0.00  0.00           H+0
HETATM   16  H   UNK     0      -0.290   3.286  -1.682  0.00  0.00           H+0
HETATM   17  H   UNK     0      -0.454   2.167   0.288  0.00  0.00           H+0
CONECT    1    2                                                            
CONECT    2    4    3    1                                                  
CONECT    3    2   12                                                       
CONECT    4    5    2   11                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    7   14                                                  
CONECT    7    6    8    9                                                  
CONECT    8    7   15                                                       
CONECT    9   11   10    7                                                  
CONECT   10    9   16                                                       
CONECT   11    9    4   17                                                  
CONECT   12    3                                                            
CONECT   13    5                                                            
CONECT   14    6                                                            
CONECT   15    8                                                            
CONECT   16   10                                                            
CONECT   17   11                                                            
MASTER        0    0    0    0    0    0    0    0   17    0   34    0
END
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3D PDB for NP0000497 (Protocatechuic acid)

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 NP0000497 (Protocatechuic acid)

[H]OC(=O)C1=C([H])C([H])=C(O[H])C(O[H])=C1[H]
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INCHI for NP0000497 (Protocatechuic acid)

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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View in JSmol
Synonyms
Chemical FormulaC7H6O4
Average Mass154.1210 Da
Monoisotopic Mass154.02661 Da
IUPAC Name3,4-dihydroxybenzoic acid
Traditional Name3,4-dihydroxybenzoic acid
CAS Registry Number99-50-3
SMILES
[H]OC(=O)C1=C([H])C([H])=C(O[H])C(O[H])=C1[H]
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
Experimental Spectra
Predicted Spectra
Spectrum TypeDescriptionDepositor IDDepositor OrganizationDepositorDeposition DateView
Chemical Shift Submissions
Spectrum TypeDescriptionDepositor EmailDepositor OrganizationDepositorDeposition DateView
1D NMR1H NMR Spectrum (1D, 600, CD3OD, simulated)bgnzk@missouri.eduSumner Lab, MU Metabolomics Center, University of Missouri, Columbia. MO, USADr. Bharat Goel2024-06-27View Spectrum
Species
Species of Origin
Species Where Detected
Species NameSourceReference
Cryptotympana sp.KNApSAcK Database
Inonotus obliquusKNApSAcK Database
Phellinus igniariusKNApSAcK Database
Pseudomonas putidaKNApSAcK Database
Chemical Taxonomy
Description 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.
KingdomOrganic compounds
Super ClassBenzenoids
ClassBenzene and substituted derivatives
Sub ClassBenzoic acids and derivatives
Direct ParentHydroxybenzoic acid derivatives
Alternative Parents
Substituents
  • Dihydroxybenzoic acid
  • Hydroxybenzoic acid
  • Benzoic acid
  • Benzoyl
  • Catechol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Carboxylic acid derivative
  • Carboxylic acid
  • Monocarboxylic acid or derivatives
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic oxide
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Physical Properties
StateSolid
Experimental Properties
PropertyValueReference
Melting Point221 °CNot Available
Boiling Point410.00 to 411.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility18.2 mg/mL at 14 °CYalkowsky, S. H., & Dannenfelser, R. M. (1992). Aquasol database of aqueous solubility. College of Pharmacy, University of Arizona, Tucson, AZ, 189.
LogP0.86Hansch CH, Leo A and Hoekman DH. "Exploring QSAR: Hydrophobic, Electronic, and Steric Constraints. Volume 1" ACS Publications (1995).
Predicted Properties
PropertyValueSource
Water Solubility12.4 g/LALOGPS
logP1.32ALOGPS
logP1.02ChemAxon
logS-1.1ALOGPS
pKa (Strongest Acidic)4.16ChemAxon
pKa (Strongest Basic)-6.3ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area77.76 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity37.28 m³·mol⁻¹ChemAxon
Polarizability13.85 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
HMDB IDHMDB0001856
DrugBank IDDB03946
Phenol Explorer Compound ID412
FoodDB IDFDB031135
KNApSAcK IDC00002668
Chemspider ID71
KEGG Compound IDC00230
BioCyc ID3-4-DIHYDROXYBENZOATE
BiGG IDNot Available
Wikipedia LinkProtocatechuic_acid
METLIN ID6350
PubChem Compound72
PDB IDNot Available
ChEBI ID36062
Good Scents IDrw1183421
References
General References
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  2. Liu KS, Tsao SM, Yin MC: In vitro antibacterial activity of roselle calyx and protocatechuic acid. Phytother Res. 2005 Nov;19(11):942-5. [PubMed:16317650 ]
  3. Ali BH, Al Wabel N, Blunden G: Phytochemical, pharmacological and toxicological aspects of Hibiscus sabdariffa L.: a review. Phytother Res. 2005 May;19(5):369-75. [PubMed:16106391 ]
  4. Petersen JR, Bissell MG, Mohammad AA: Laser induced resonance energy transfer--a novel approach towards achieving high sensitivity in capillary electrophoresis. I. Clinical diagnostic application. J Chromatogr A. 1996 Sep 13;744(1-2):37-44. [PubMed:8843662 ]
  5. Babich H, Sedletcaia A, Kenigsberg B: In vitro cytotoxicity of protocatechuic acid to cultured human cells from oral tissue: involvement in oxidative stress. Pharmacol Toxicol. 2002 Nov;91(5):245-53. [PubMed:12570031 ]
  6. Szumilo J: [Protocatechuic acid in cancer prevention]. Postepy Hig Med Dosw (Online). 2005;59:608-15. [PubMed:16407799 ]