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Showing metabocard for Pyrocatechol (HMDB0000957)

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Record Information
Version5.0
StatusDetected and Quantified
Creation Date2005-11-16 15:48:42 UTC
Update Date2023-02-21 17:15:20 UTC
HMDB IDHMDB0000957
Secondary Accession Numbers
  • HMDB00957
Metabolite Identification
Common NamePyrocatechol
DescriptionPyrocatechol, often known as catechol or benzene-1,2-diol, is a benzenediol, with formula C6H4(OH)2. It was first prepared in 1839 by H. Reinsch by distilling catechin (the juice of Mimosa catechu). This colourless compound occurs naturally, but about 20000 tons are manufactured each year, mainly as precursors to pesticides, flavors, and fragrances. Its sulfonic acid is often present in the urine of many mammals. Small amounts of catechol occur naturally in fruits and vegetables, along with the enzyme polyphenol oxidase. Upon mixing the enzyme with the substrate and exposure to oxygen (as when a potato or apple is cut), the colorless catechol oxidizes to reddish-brown benzoquinone derivatives. The enzyme is inactivated by adding an acid, such as lemon juice, or by refrigeration. Excluding oxygen also prevents the browning reaction. Catechol melts at 28 °C and boils at 250 °C. It is employed in medicine as an expectorant. The dimethyl ether or veratrol is also used in medicine. Many other pyrocatechin derivatives have been suggested for therapeutic application. Pyrocatechol has also been found to be a microbial metabolite in Escherichia, Mycobacterium and Pseudomonas (PMID:19300498 ; PMID:25281236 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0000957 (Pyrocatechol)

  Mrv1652309272007412D          

  8  8  0  0  0  0            999 V2000
    0.0000    0.8250    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
    0.7145    0.4125    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   -0.8250    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
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  1  3  2  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  5  1  0  0  0  0
  6  2  2  0  0  0  0
  1  8  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
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3D MOL for HMDB0000957 (Pyrocatechol)

HMDB0000957
     RDKit          3D
Pyrocatechol
 14 14  0  0  0  0  0  0  0  0999 V2000
    1.6743   -1.6790    0.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5996   -0.8057    0.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136   -1.2721    0.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7721   -0.4071   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6088    0.9633   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3196    1.4455   -0.0295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7698    0.5578   -0.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0526    1.0989   -0.0109 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6461   -1.4306    0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8196   -2.3565    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7883   -0.8049    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4704    1.6115   -0.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324    2.5191   -0.0492 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8826    0.5599    0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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3D SDF for HMDB0000957 (Pyrocatechol)

  Mrv1652309272007412D          

  8  8  0  0  0  0            999 V2000
    0.0000    0.8250    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
    0.7145    0.4125    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   -0.8250    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
    1.4289    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    1.6500    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  1  3  2  0  0  0  0
  4  3  1  0  0  0  0
  5  4  2  0  0  0  0
  6  5  1  0  0  0  0
  6  2  2  0  0  0  0
  1  8  1  0  0  0  0
  3  7  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0000957

> <DATABASE_NAME>
hmdb

> <SMILES>
OC1=C(O)C=CC=C1

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H

> <INCHI_KEY>
YCIMNLLNPGFGHC-UHFFFAOYSA-N

> <FORMULA>
C6H6O2

> <MOLECULAR_WEIGHT>
110.1106

> <EXACT_MASS>
110.036779436

> <JCHEM_ACCEPTOR_COUNT>
2

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.692303526357614

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
benzene-1,2-diol

> <ALOGPS_LOGP>
0.74

> <JCHEM_LOGP>
1.3661151726666665

> <ALOGPS_LOGS>
-0.17

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.794732100904419

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.342309260967141

> <JCHEM_PKA_STRONGEST_BASIC>
-6.287220763519362

> <JCHEM_POLAR_SURFACE_AREA>
40.46

> <JCHEM_REFRACTIVITY>
30.019799999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
7.50e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
catechol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0000957 (Pyrocatechol)

HMDB0000957
     RDKit          3D
Pyrocatechol
 14 14  0  0  0  0  0  0  0  0999 V2000
    1.6743   -1.6790    0.0407 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5996   -0.8057    0.0185 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7136   -1.2721    0.0210 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7721   -0.4071   -0.0010 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6088    0.9633   -0.0266 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3196    1.4455   -0.0295 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7698    0.5578   -0.0069 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0526    1.0989   -0.0109 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6461   -1.4306    0.0408 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8196   -2.3565    0.0413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7883   -0.8049    0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4704    1.6115   -0.0434 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1324    2.5191   -0.0492 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8826    0.5599    0.0036 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  2  0
  3  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  7  8  1  0
  7  2  1  0
  1  9  1  0
  3 10  1  0
  4 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
M  END
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PDB for HMDB0000957 (Pyrocatechol)

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       0.000   1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      -1.334   0.770   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.770   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       2.667   1.540   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   3.080   0.000  0.00  0.00           O+0
CONECT    1    2    3    8                                                  
CONECT    2    1    6                                                       
CONECT    3    1    4    7                                                  
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    2                                                       
CONECT    7    3                                                            
CONECT    8    1                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   16    0
END
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3D PDB for HMDB0000957 (Pyrocatechol)

COMPND    HMDB0000957
HETATM    1  O1  UNL     1       1.674  -1.679   0.041  1.00  0.00           O  
HETATM    2  C1  UNL     1       0.600  -0.806   0.019  1.00  0.00           C  
HETATM    3  C2  UNL     1      -0.714  -1.272   0.021  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.772  -0.407  -0.001  1.00  0.00           C  
HETATM    5  C4  UNL     1      -1.609   0.963  -0.027  1.00  0.00           C  
HETATM    6  C5  UNL     1      -0.320   1.445  -0.029  1.00  0.00           C  
HETATM    7  C6  UNL     1       0.770   0.558  -0.007  1.00  0.00           C  
HETATM    8  O2  UNL     1       2.053   1.099  -0.011  1.00  0.00           O  
HETATM    9  H1  UNL     1       2.646  -1.431   0.041  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.820  -2.357   0.041  1.00  0.00           H  
HETATM   11  H3  UNL     1      -2.788  -0.805   0.002  1.00  0.00           H  
HETATM   12  H4  UNL     1      -2.470   1.612  -0.043  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.132   2.519  -0.049  1.00  0.00           H  
HETATM   14  H6  UNL     1       2.883   0.560   0.004  1.00  0.00           H  
CONECT    1    2    9
CONECT    2    3    3    7
CONECT    3    4   10
CONECT    4    5    5   11
CONECT    5    6   12
CONECT    6    7    7   13
CONECT    7    8
CONECT    8   14
END
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SMILES for HMDB0000957 (Pyrocatechol)

OC1=C(O)C=CC=C1
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INCHI for HMDB0000957 (Pyrocatechol)

InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H6O2
Average Molecular Weight110.1106
Monoisotopic Molecular Weight110.036779436
IUPAC Namebenzene-1,2-diol
Traditional Namecatechol
CAS Registry Number120-80-9
SMILES
OC1=C(O)C=CC=C1
InChI Identifier
InChI=1S/C6H6O2/c7-5-3-1-2-4-6(5)8/h1-4,7-8H
InChI KeyYCIMNLLNPGFGHC-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as catechols. Catechols are compounds containing a 1,2-benzenediol moiety.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub ClassBenzenediols
Direct ParentCatechols
Alternative Parents
Substituents
  • Catechol
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocyclic benzene moiety
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effect
Health effect
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Industrial applicationEnvironmental roleBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point105 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility461 mg/mLNot Available
LogP0.88HANSCH,C ET AL. (1995)
Experimental Chromatographic Properties

Experimental Collision Cross Sections

Adduct TypeData SourceCCS Value (Å2)Reference
[M-H]-Not Available115.7http://allccs.zhulab.cn/database/detail?ID=AllCCS00002104
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Feces
  • Saliva
  • Urine
Tissue Locations
  • Adipose Tissue
  • Adrenal Gland
  • Bone Marrow
  • Brain
  • Intestine
  • Liver
  • Neuron
  • Prostate
Pathways
Normal Concentrations
Abnormal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothAutosomal dominant polycystic kidney disease (ADPKD) details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothBladder cancer details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Schizophrenia		 details
Associated Disorders and Diseases
Disease References
Autosomal dominant polycystic kidney disease
  1. Gronwald W, Klein MS, Zeltner R, Schulze BD, Reinhold SW, Deutschmann M, Immervoll AK, Boger CA, Banas B, Eckardt KU, Oefner PJ: Detection of autosomal dominant polycystic kidney disease by NMR spectroscopic fingerprinting of urine. Kidney Int. 2011 Jun;79(11):1244-53. doi: 10.1038/ki.2011.30. Epub 2011 Mar 9. [PubMed:21389975 ]
Schizophrenia
  1. Yang J, Chen T, Sun L, Zhao Z, Qi X, Zhou K, Cao Y, Wang X, Qiu Y, Su M, Zhao A, Wang P, Yang P, Wu J, Feng G, He L, Jia W, Wan C: Potential metabolite markers of schizophrenia. Mol Psychiatry. 2013 Jan;18(1):67-78. doi: 10.1038/mp.2011.131. Epub 2011 Oct 25. [PubMed:22024767 ]
Associated OMIM IDs
  • 601313 (Autosomal dominant polycystic kidney disease)
  • 181500 (Schizophrenia)
DrugBank IDDB02232
Phenol Explorer Compound ID654
FooDB IDFDB001512
KNApSAcK IDC00002644
Chemspider ID13837760
KEGG Compound IDC15571
BioCyc IDCATECHOL
BiGG IDNot Available
Wikipedia LinkCatechol
METLIN ID282
PubChem Compound289
PDB IDNot Available
ChEBI ID18135
Food Biomarker OntologyNot Available
VMH IDCATECHOL
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceLauterbach, Manfred; Zimmermann, Volker; Jaeger, Guenter; Radig, Wolfram; Adam, Johannes; Blady, Regina. Extraction and purification of pyrocatechol. Ger. (East) (1986), 4 pp.
Material Safety Data Sheet (MSDS)Not Available
General References

Enzymes

Enzyme Details
1. Aldo-keto reductase family 1 member C4
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the transformation of the potent androgen dihydrotestosterone (DHT) into the less active form, 5-alpha-androstan-3-alpha,17-beta-diol (3-alpha-diol). Also has some 20-alpha-hydroxysteroid dehydrogenase activity. The biotransformation of the pesticide chlordecone (kepone) to its corresponding alcohol leads to increased biliary excretion of the pesticide and concomitant reduction of its neurotoxicity since bile is the major excretory route.
Gene Name:
AKR1C4
Uniprot ID:
P17516
Molecular weight:
37094.57
Enzyme Details
2. Catechol O-methyltransferase
General function:
Involved in magnesium ion binding
Specific function:
Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones. Also shortens the biological half-lives of certain neuroactive drugs, like L-DOPA, alpha-methyl DOPA and isoproterenol.
Gene Name:
COMT
Uniprot ID:
P21964
Molecular weight:
30036.77
Reactions
Pyrocatechol → Guaiacoldetails
Enzyme Details
3. Sulfotransferase 1A3/1A4
General function:
Involved in 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:
P50224
Molecular weight:
34195.96
Enzyme Details
4. Aldo-keto reductase family 1 member C3
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the conversion of aldehydes and ketones to alcohols. Catalyzes the reduction of prostaglandin (PG) D2, PGH2 and phenanthrenequinone (PQ) and the oxidation of 9-alpha,11-beta-PGF2 to PGD2. Functions as a bi-directional 3-alpha-, 17-beta- and 20-alpha HSD. Can interconvert active androgens, estrogens and progestins with their cognate inactive metabolites. Preferentially transforms androstenedione (4-dione) to testosterone.
Gene Name:
AKR1C3
Uniprot ID:
P42330
Molecular weight:
36866.91
Reactions
trans-1,2-Dihydrobenzene-1,2-diol + NADP → Pyrocatechol + NADPHdetails
Enzyme Details
5. Aldo-keto reductase family 1 member C1
General function:
Involved in oxidoreductase activity
Specific function:
Converts progesterone to its inactive form, 20-alpha-dihydroxyprogesterone (20-alpha-OHP). In the liver and intestine, may have a role in the transport of bile. May have a role in monitoring the intrahepatic bile acid concentration. Has a low bile-binding ability. May play a role in myelin formation.
Gene Name:
AKR1C1
Uniprot ID:
Q04828
Molecular weight:
36788.02
Reactions
trans-1,2-Dihydrobenzene-1,2-diol + NADP → Pyrocatechol + NADPHdetails
Enzyme Details
6. Aldo-keto reductase family 1 member C2
General function:
Involved in oxidoreductase activity
Specific function:
Works in concert with the 5-alpha/5-beta-steroid reductases to convert steroid hormones into the 3-alpha/5-alpha and 3-alpha/5-beta-tetrahydrosteroids. Catalyzes the inactivation of the most potent androgen 5-alpha-dihydrotestosterone (5-alpha-DHT) to 5-alpha-androstane-3-alpha,17-beta-diol (3-alpha-diol). Has a high bile-binding ability.
Gene Name:
AKR1C2
Uniprot ID:
P52895
Molecular weight:
15747.91
Reactions
trans-1,2-Dihydrobenzene-1,2-diol + NADP → Pyrocatechol + NADPHdetails
Enzyme Details
7. 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
Pyrocatechol → 3,4,5-trihydroxy-6-(2-hydroxyphenoxy)oxane-2-carboxylic aciddetails
Enzyme Details
8. Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
DHDH
Uniprot ID:
Q9UQ10
Molecular weight:
36381.705
Reactions
trans-1,2-Dihydrobenzene-1,2-diol + NADP → Pyrocatechol + NADPHdetails
Enzyme Details
9. Transmembrane O-methyltransferase
General function:
Involved in O-methyltransferase activity
Specific function:
Catalyzes the O-methylation, and thereby the inactivation, of catecholamine neurotransmitters and catechol hormones (By similarity). Required for auditory function.
Gene Name:
LRTOMT
Uniprot ID:
Q8WZ04
Molecular weight:
32154.43