NP-MRD: Showing NP-Card for Pyrogallol (NP0004774)

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Record Information

Version

2.0

Created at

2020-12-09 02:11:32 UTC

Updated at

2024-09-03 04:19:08 UTC

NP-MRD ID

NP0004774

Natural Product DOI

https://doi.org/10.57994/1647

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Pyrogallol

Provided By

NPAtlas

Description

1,2,3-Trihydroxybenzene, also known as 1,2,3-benzenetriol or pyrogallic acid, belongs to the class of organic compounds known as 5-unsubstituted pyrrogallols. These are pyrrogallols that are unsubstituted at th5-position of the benzene ring. 1,2,3-Trihydroxybenzene is a primary metabolite. Primary metabolites are metabolically or physiologically essential metabolites. They are directly involved in an organism’s growth, development or reproduction. Pyrogallol is found in Agave americana, Bistorta officinalis, Bixa orellana, Erica arborea, Euphorbia tithymaloides, Hamamelis virginiana, Nigella glandulifera, Penicillium, Penicillium solitum, Peperomia heyneana, Populus deltoides, Quercus robur and Saxifraga stolonifera. Pyrogallol was first documented in 1999 (PMID: 10427737). Based on a literature review a small amount of articles have been published on 1,2,3-Trihydroxybenzene (PMID: 18506365) (PMID: 18760383) (PMID: 19948158).

Structure

MOL 3D MOL SDF 3D SDF PDB SMILES InChI


  Mrv1652306242121113D          

 15 15  0  0  0  0            999 V2000
    2.4550   -0.1044    0.1200 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0827   -0.2798    0.0409 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4830   -1.5192   -0.0534 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8978   -1.6476   -0.1305 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7052   -0.5312   -0.1144 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1189    0.7373   -0.0193 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9096    1.8782   -0.0011 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2669    0.8298    0.0563 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8499    2.0736    0.1499 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1220   -0.8428    0.1162 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1026   -2.3998   -0.0669 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3358   -2.6433   -0.2040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7810   -0.5782   -0.1717 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4376    2.7691    0.0688 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8238    2.2585    0.2092 H   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
  3  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
  8  2  1  0  0  0  0
  1 10  1  0  0  0  0
  3 11  1  0  0  0  0
  4 12  1  0  0  0  0
  5 13  1  0  0  0  0
  7 14  1  0  0  0  0
  9 15  1  0  0  0  0
M  END
> <DATABASE_ID>
NP0004774

> <DATABASE_NAME>
NP-MRD

> <SMILES>
[H]OC1=C([H])C([H])=C([H])C(O[H])=C1O[H]

> <INCHI_IDENTIFIER>
InChI=1S/C6H6O3/c7-4-2-1-3-5(8)6(4)9/h1-3,7-9H

> <INCHI_KEY>
WQGWDDDVZFFDIG-UHFFFAOYSA-N

> <FORMULA>
C6H6O3

> <MOLECULAR_WEIGHT>
126.11

> <EXACT_MASS>
126.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.574131051791344

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
benzene-1,2,3-triol

> <ALOGPS_LOGP>
0.34

> <JCHEM_LOGP>
1.0625498509999998

> <ALOGPS_LOGS>
-0.39

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
11.295519087549843

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.937265402300763

> <JCHEM_PKA_STRONGEST_BASIC>
-5.9945422818884255

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
32.000699999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.18e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pyrogallol

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-JUN-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-JUN-21         0                                  
HETATM    1  O   UNK     0       2.455  -0.104   0.120  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.083  -0.280   0.041  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.483  -1.519  -0.053  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.898  -1.648  -0.131  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.705  -0.531  -0.114  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.119   0.737  -0.019  0.00  0.00           C+0
HETATM    7  O   UNK     0      -1.910   1.878  -0.001  0.00  0.00           O+0
HETATM    8  C   UNK     0       0.267   0.830   0.056  0.00  0.00           C+0
HETATM    9  O   UNK     0       0.850   2.074   0.150  0.00  0.00           O+0
HETATM   10  H   UNK     0       3.122  -0.843   0.116  0.00  0.00           H+0
HETATM   11  H   UNK     0       1.103  -2.400  -0.067  0.00  0.00           H+0
HETATM   12  H   UNK     0      -1.336  -2.643  -0.204  0.00  0.00           H+0
HETATM   13  H   UNK     0      -2.781  -0.578  -0.172  0.00  0.00           H+0
HETATM   14  H   UNK     0      -1.438   2.769   0.069  0.00  0.00           H+0
HETATM   15  H   UNK     0       1.824   2.259   0.209  0.00  0.00           H+0
CONECT    1    2   10                                                       
CONECT    2    1    3    8                                                  
CONECT    3    2    4   11                                                  
CONECT    4    3    5   12                                                  
CONECT    5    4    6   13                                                  
CONECT    6    5    7    8                                                  
CONECT    7    6   14                                                       
CONECT    8    6    9    2                                                  
CONECT    9    8   15                                                       
CONECT   10    1                                                            
CONECT   11    3                                                            
CONECT   12    4                                                            
CONECT   13    5                                                            
CONECT   14    7                                                            
CONECT   15    9                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   30    0
END

View in JSmol View NMR Assignments

Synonyms

Value	Source
1,2,3-Benzenetriol	ChEBI
Benzene-1,2,3-triol	ChEBI
Pyrogallic acid	ChEBI
Pyrogallol	Kegg
Pyrogallate	Generator
1,2,3-Benzenetriol (acd/name 4.0)	HMDB
1,2,3-Trihydroxy-benzene	HMDB
1,2,3-Trihydroxybenzen	HMDB
2,3-Dihydroxyphenol	HMDB
C.I. oxidation base 32	HMDB
Fouramine base ap	HMDB
Fouramine brown ap	HMDB
Fourrine 85	HMDB
Fourrine PG	HMDB
Phenol	HMDB
Piral	HMDB
Pyro	HMDB
Acid, pyrogallic	MeSH, HMDB

Chemical Formula

C₆H₆O₃

Average Mass

126.1100 Da

Monoisotopic Mass

126.03169 Da

IUPAC Name

benzene-1,2,3-triol

Traditional Name

pyrogallol

CAS Registry Number

Not Available

SMILES

OC1=CC=CC(O)=C1O

InChI Identifier

InChI=1S/C6H6O3/c7-4-2-1-3-5(8)6(4)9/h1-3,7-9H

InChI Key

WQGWDDDVZFFDIG-UHFFFAOYSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-23	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-23	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-23	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-23	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, CD3OD, experimental)	bgnzk@missouri.edu	MU Metabolomics Center, University of Missouri, Columbia. MO, USA	Dr. Bharat Goel	2024-01-23	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 25 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 252 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 50 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 75 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 126 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 151 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 176 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 201 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 226 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Chemical Shift Submissions

Not Available

Species

Species of Origin

Species Name	Source	Reference
Agave americana	LOTUS Database	35616633
Bistorta officinalis	LOTUS Database	35616633
Bixa orellana	LOTUS Database	35616633
Ceratonia siliqua	KNApSAcK Database	22123792
Coffea arabica L.	FooDB	PHENOL EXPLORER
Coffea canephora	FooDB	PHENOL EXPLORER
Erica arborea	LOTUS Database	35616633
Euphorbia tithymaloides	LOTUS Database	35616633
Geranium thunbergii	KNApSAcK Database	22123792
Geum urbanum	KNApSAcK Database	22123792
Gunnera perpensa	KNApSAcK Database	22123792
Hamamelis virginiana	LOTUS Database	35616633
Lagerstroemia speciosa	KNApSAcK Database	22123792
Nigella glandulifera	LOTUS Database	35616633
Penicillium	NPAtlas	13535672
Penicillium solitum	LOTUS Database	35616633
Peperomia duclouxii	KNApSAcK Database	22123792
Peperomia heyneana	LOTUS Database	35616633
Phyllanthus emblica	KNApSAcK Database	22123792
Phyllanthus reticulatus	KNApSAcK Database	22123792
Populus deltoides	LOTUS Database	35616633
Posidonia oceanica	KNApSAcK Database	22123792
Quercus robur	LOTUS Database	35616633
Rheum maximoviczii	KNApSAcK Database	22123792
Rheum maximowiczii	KNApSAcK Database	22123792
Rosa spp.	KNApSAcK Database	22123792
Rubus rigididus	KNApSAcK Database	22123792
Rubus rigidus	KNApSAcK Database	22123792
Saxifraga stolonifera	LOTUS Database	35616633
Senecio nemorensis	KNApSAcK Database	22123792
Statice gmelinii	KNApSAcK Database	22123792

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 5-unsubstituted pyrrogallols. These are pyrrogallols that are unsubstituted at th5-position of the benzene ring.

Kingdom

Organic compounds

Super Class

Benzenoids

Class

Phenols

Sub Class

Benzenetriols and derivatives

Direct Parent

5-unsubstituted pyrrogallols

Alternative Parents

Not Available

Substituents

Not Available

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	0.47 mg/L @ 25 °C (est)	The Good Scents Company Information System
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	0.34	ALOGPS
logP	1.06	ChemAxon
logS	-0.39	ALOGPS
pKa (Strongest Acidic)	8.94	ChemAxon
pKa (Strongest Basic)	-6	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	60.69 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	32 m³·mol⁻¹	ChemAxon
Polarizability	11.57 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

NPAtlas ID

NPA005967

HMDB ID

HMDB0013674

DrugBank ID

Not Available

Phenol Explorer Compound ID

FoodDB ID

KNApSAcK ID

Chemspider ID

KEGG Compound ID

BioCyc ID

BiGG ID

Not Available

Wikipedia Link

Pyrogallol

METLIN ID

Not Available

PubChem Compound

PDB ID

ChEBI ID

Good Scents ID

References

General References

Kumar RA, Gunasekaran P, Lakshmanan M: Biodegradation of tannic acid by Citrobacter freundii isolated from a tannery effluent. J Basic Microbiol. 1999;39(3):161-8. [PubMed:10427737 ]
Han YH, Kim SZ, Kim SH, Park WH: Pyrogallol as a glutathione depletor induces apoptosis in HeLa cells. Int J Mol Med. 2008 Jun;21(6):721-30. [PubMed:18506365 ]
Nicolis E, Lampronti I, Dechecchi MC, Borgatti M, Tamanini A, Bianchi N, Bezzerri V, Mancini I, Giri MG, Rizzotti P, Gambari R, Cabrini G: Pyrogallol, an active compound from the medicinal plant Emblica officinalis, regulates expression of pro-inflammatory genes in bronchial epithelial cells. Int Immunopharmacol. 2008 Dec 10;8(12):1672-80. doi: 10.1016/j.intimp.2008.08.001. Epub 2008 Aug 27. [PubMed:18760383 ]
Upadhyay G, Gupta SP, Prakash O, Singh MP: Pyrogallol-mediated toxicity and natural antioxidants: triumphs and pitfalls of preclinical findings and their translational limitations. Chem Biol Interact. 2010 Feb 12;183(3):333-40. doi: 10.1016/j.cbi.2009.11.028. Epub 2009 Dec 3. [PubMed:19948158 ]

Showing NP-Card for Pyrogallol (NP0004774)

MOL for NP0004774 (Pyrogallol)

3D MOL for NP0004774 (Pyrogallol)

3D SDF for NP0004774 (Pyrogallol)

3D-SDF for NP0004774 (Pyrogallol)

PDB for NP0004774 (Pyrogallol)

3D PDB for NP0004774 (Pyrogallol)

SMILES for NP0004774 (Pyrogallol)

INCHI for NP0004774 (Pyrogallol)

Structure for NP0004774 (Pyrogallol)

3D Structure for NP0004774 (Pyrogallol)