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Showing metabocard for 3-Hydroxybenzoic acid (HMDB0002466)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2006-05-22 14:17:54 UTC
Update Date2023-02-21 17:16:25 UTC
HMDB IDHMDB0002466
Secondary Accession Numbers
  • HMDB02466
Metabolite Identification
Common Name3-Hydroxybenzoic acid
Description3-Hydroxybenzoic acid, also known as 3-hydroxybenzoate or 3-carboxyphenol, 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. 3-Hydroxybenzoic acid exists in all living organisms, ranging from bacteria to humans. Outside of the human body, 3-hydroxybenzoic acid is found, on average, in the highest concentration in american cranberries and beers. 3-hydroxybenzoic acid has also been detected, but not quantified in a few different foods, such as bilberries, citrus, and corns. As well, 3-Hydroxybenzoic Acid can be found in the pineapple fruit. It can also be formed by a Pseudomonas species from 3-Chlorobenzoic acid. 3-Hydroxybenzoic acid is a monohydroxybenzoic acid. 3-Hydroxybenzoic acid can be obtained by the alkali fusion of 3-sulfobenzoic acid between 210-220 °C. 3-Hydroxybenzoic acid is a component of castoreum, the exudate from the castor sacs of the mature North American beaver (Castor canadensis) and the European beaver (Castor fiber), used in perfumery.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0002466 (3-Hydroxybenzoic acid)

3-Hydroxybenzoic acid
  Mrv1652305261923572D          

 10 10  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   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
    0.0000    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
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  4 10  1  0  0  0  0
M  END
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3D MOL for HMDB0002466 (3-Hydroxybenzoic acid)

HMDB0002466
     RDKit          3D
3-Hydroxybenzoic acid
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.1993   -2.0914   -0.3568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0898   -0.8576   -0.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2065   -0.0751   -0.2699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7755   -0.2728   -0.0808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6338    1.1117    0.0495 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6154    1.6700    0.2030 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7478    0.8836    0.2317 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6029   -0.4860    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7742   -1.2683    0.1348 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3663   -1.0723   -0.0524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7482    0.2300    0.5099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4758    1.7722    0.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7708    2.7419    0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7467    1.2930    0.3513 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046   -1.4256   -0.7723 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004   -2.1535   -0.1504 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
  8  9  1  0
  8 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  9 15  1  0
 10 16  1  0
M  END
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3D SDF for HMDB0002466 (3-Hydroxybenzoic acid)

3-Hydroxybenzoic acid
  Mrv1652305261923572D          

 10 10  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
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.4125    0.0000 O   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
    0.0000    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
  6  7  1  0  0  0  0
  6  8  2  0  0  0  0
  8  9  1  0  0  0  0
  9 10  2  0  0  0  0
  4 10  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0002466

> <DATABASE_NAME>
hmdb

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H6O3/c8-6-3-1-2-5(4-6)7(9)10/h1-4,8H,(H,9,10)

> <INCHI_KEY>
IJFXRHURBJZNAO-UHFFFAOYSA-N

> <FORMULA>
C7H6O3

> <MOLECULAR_WEIGHT>
138.122

> <EXACT_MASS>
138.031694053

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
12.915865293587439

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
3-hydroxybenzoic acid

> <ALOGPS_LOGP>
1.81

> <JCHEM_LOGP>
1.3272634023333332

> <ALOGPS_LOGS>
-1.13

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.54879634453029

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.844596909709927

> <JCHEM_PKA_STRONGEST_BASIC>
-6.007037034515304

> <JCHEM_POLAR_SURFACE_AREA>
57.53

> <JCHEM_REFRACTIVITY>
35.2951

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
3-hydroxybenzoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0002466 (3-Hydroxybenzoic acid)

HMDB0002466
     RDKit          3D
3-Hydroxybenzoic acid
 16 16  0  0  0  0  0  0  0  0999 V2000
   -2.1993   -2.0914   -0.3568 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0898   -0.8576   -0.2421 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2065   -0.0751   -0.2699 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7755   -0.2728   -0.0808 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6338    1.1117    0.0495 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6154    1.6700    0.2030 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7478    0.8836    0.2317 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6029   -0.4860    0.1024 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7742   -1.2683    0.1348 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3663   -1.0723   -0.0524 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7482    0.2300    0.5099 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4758    1.7722    0.0346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7708    2.7419    0.3077 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7467    1.2930    0.3513 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2046   -1.4256   -0.7723 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3004   -2.1535   -0.1504 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
  8  9  1  0
  8 10  2  0
 10  4  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  7 14  1  0
  9 15  1  0
 10 16  1  0
M  END
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PDB for HMDB0002466 (3-Hydroxybenzoic acid)

HEADER    PROTEIN                                 26-MAY-19   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 3-Hydroxybenzoic acid                             
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAY-19         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  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       4.001  -0.770   0.000  0.00  0.00           O+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  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   10                                                  
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9    4                                                       
MASTER        0    0    0    0    0    0    0    0   10    0   20    0
END
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3D PDB for HMDB0002466 (3-Hydroxybenzoic acid)

COMPND    HMDB0002466
HETATM    1  O1  UNL     1      -2.199  -2.091  -0.357  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.090  -0.858  -0.242  1.00  0.00           C  
HETATM    3  O2  UNL     1      -3.207  -0.075  -0.270  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.776  -0.273  -0.081  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.634   1.112   0.049  1.00  0.00           C  
HETATM    6  C4  UNL     1       0.615   1.670   0.203  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.748   0.884   0.232  1.00  0.00           C  
HETATM    8  C6  UNL     1       1.603  -0.486   0.102  1.00  0.00           C  
HETATM    9  O3  UNL     1       2.774  -1.268   0.135  1.00  0.00           O  
HETATM   10  C7  UNL     1       0.366  -1.072  -0.052  1.00  0.00           C  
HETATM   11  H1  UNL     1      -3.748   0.230   0.510  1.00  0.00           H  
HETATM   12  H2  UNL     1      -1.476   1.772   0.035  1.00  0.00           H  
HETATM   13  H3  UNL     1       0.771   2.742   0.308  1.00  0.00           H  
HETATM   14  H4  UNL     1       2.747   1.293   0.351  1.00  0.00           H  
HETATM   15  H5  UNL     1       3.205  -1.426  -0.772  1.00  0.00           H  
HETATM   16  H6  UNL     1       0.300  -2.153  -0.150  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3   11
CONECT    4    5    5   10
CONECT    5    6   12
CONECT    6    7    7   13
CONECT    7    8   14
CONECT    8    9   10   10
CONECT    9   15
CONECT   10   16
END
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SMILES for HMDB0002466 (3-Hydroxybenzoic acid)

OC(=O)C1=CC(O)=CC=C1
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INCHI for HMDB0002466 (3-Hydroxybenzoic acid)

InChI=1S/C7H6O3/c8-6-3-1-2-5(4-6)7(9)10/h1-4,8H,(H,9,10)
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC7H6O3
Average Molecular Weight138.122
Monoisotopic Molecular Weight138.031694053
IUPAC Name3-hydroxybenzoic acid
Traditional Name3-hydroxybenzoic acid
CAS Registry Number99-06-9
SMILES
OC(=O)C1=CC(O)=CC=C1
InChI Identifier
InChI=1S/C7H6O3/c8-6-3-1-2-5(4-6)7(9)10/h1-4,8H,(H,9,10)
InChI KeyIJFXRHURBJZNAO-UHFFFAOYSA-N
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
  • Hydroxybenzoic acid
  • Benzoic acid
  • Benzoyl
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Biological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point202 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility7.25 mg/mL at 25 °CNot Available
LogP1.50HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available125.399http://allccs.zhulab.cn/database/detail?ID=AllCCS00000304
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Colorectal cancer		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothColorectal Cancer details
Associated Disorders and Diseases
Disease References
Colorectal cancer
  1. Brown DG, Rao S, Weir TL, O'Malia J, Bazan M, Brown RJ, Ryan EP: Metabolomics and metabolic pathway networks from human colorectal cancers, adjacent mucosa, and stool. Cancer Metab. 2016 Jun 6;4:11. doi: 10.1186/s40170-016-0151-y. eCollection 2016. [PubMed:27275383 ]
  2. Sinha R, Ahn J, Sampson JN, Shi J, Yu G, Xiong X, Hayes RB, Goedert JJ: Fecal Microbiota, Fecal Metabolome, and Colorectal Cancer Interrelations. PLoS One. 2016 Mar 25;11(3):e0152126. doi: 10.1371/journal.pone.0152126. eCollection 2016. [PubMed:27015276 ]
  3. Goedert JJ, Sampson JN, Moore SC, Xiao Q, Xiong X, Hayes RB, Ahn J, Shi J, Sinha R: Fecal metabolomics: assay performance and association with colorectal cancer. Carcinogenesis. 2014 Sep;35(9):2089-96. doi: 10.1093/carcin/bgu131. Epub 2014 Jul 18. [PubMed:25037050 ]
Associated OMIM IDs
DrugBank IDNot Available
Phenol Explorer Compound ID429
FooDB IDFDB010507
KNApSAcK IDC00040822
Chemspider ID7142
KEGG Compound IDC00587
BioCyc ID3-HYDROXYBENZOATE
BiGG IDNot Available
Wikipedia Link3-Hydroxybenzoic_acid
METLIN ID6690
PubChem Compound7420
PDB IDNot Available
ChEBI ID30764
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceUngnade, H. E.; Henick, A. S. Preparation of m-hydroxybenzoic acid. Journal of the American Chemical Society (1942), 64 1737-8.
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Liu JH, Smith PC: Direct analysis of salicylic acid, salicyl acyl glucuronide, salicyluric acid and gentisic acid in human plasma and urine by high-performance liquid chromatography. J Chromatogr B Biomed Appl. 1996 Jan 12;675(1):61-70. [PubMed:8634769 ]
  2. Ito S, Maruta K, Imai Y, Kato T, Ito M, Nakajima S, Fujita K, Kurahashi T: Urinary p-aminobenzoic acid determined in the pancreatic function test by liquid chromatography, with electrochemical detection. Clin Chem. 1982 Feb;28(2):323-6. [PubMed:6976857 ]
  3. Dubois H, Delvoux B, Ehrhardt V, Greiling H: An enzymic assay for uric acid in serum and urine compared with HPLC. J Clin Chem Clin Biochem. 1989 Mar;27(3):151-6. [PubMed:2708944 ]
  4. Koistinen VM (2019). Effects of Food Processing and Gut Microbial Metabolism on Whole Grain Phytochemicals: A Metabolomics Approach. In Publications of the University of Eastern Finland. Dissertations in Health Sciences., no 510 (pp. 26-58). University of Eastern Finland. [ISBN:978-952-61-3088-0 ]
  5. http://www.chemicalland21.com/lifescience/phar/m-HYDROXYBENZOIC%20ACID.htm [Link]

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
3-Hydroxybenzoic acid → 6-(3-carboxyphenoxy)-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
3-Hydroxybenzoic acid → 3,4,5-trihydroxy-6-(3-hydroxybenzoyloxy)oxane-2-carboxylic aciddetails
Enzyme Details
2. Glycine N-acyltransferase
General function:
Involved in glycine N-acyltransferase activity
Specific function:
Mitochondrial acyltransferase which transfers an acyl group to the N-terminus of glycine and glutamine, although much less efficiently. Can conjugate numerous substrates to form a variety of N-acylglycines, with a preference for benzoyl-CoA over phenylacetyl-CoA as acyl donors. Thereby detoxify xenobiotics, such as benzoic acid or salicylic acid, and endogenous organic acids, such as isovaleric acid.
Gene Name:
GLYAT
Uniprot ID:
Q6IB77
Molecular weight:
18506.33
Reactions
3-Hydroxybenzoic acid → 3-Hydroxyhippuric aciddetails
Enzyme Details
3. Sulfotransferase 1A3
General function:
sulfotransferase activity
Specific function:
Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) as sulfonate donor to catalyze the sulfate conjugation of phenolic monoamines (neurotransmitters such as dopamine, norepinephrine and serotonin) and phenolic and catechol drugs.
Gene Name:
SULT1A3
Uniprot ID:
P0DMM9
Molecular weight:
34195.96
Reactions
3-Hydroxybenzoic acid → 3-hydroxybenzoic acid-3-O-sulphatedetails