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Showing metabocard for 1,3,5-Trihydroxybenzene (HMDB0013675)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-04-03 14:10:30 UTC
Update Date2023-02-21 17:18:00 UTC
HMDB IDHMDB0013675
Secondary Accession Numbers
  • HMDB13675
Metabolite Identification
Common Name1,3,5-Trihydroxybenzene
Description1,3,5-Trihydroxybenzene, also known as 1,3,5-benzenetriol or benzene-1,3,5-triol, belongs to the class of organic compounds known as phloroglucinols and derivatives. Phloroglucinols and derivatives are compounds containing a phloroglucinol (benzene-1,3,5-triol) moiety, which consists of a benzene ring bearing one hydroxyl group at positions 1,3, and 5. 1,3,5-Trihydroxybenzene is found, on average, in the highest concentration within garden onions (Allium cepa). 1,3,5-Trihydroxybenzene has also been detected, but not quantified in, several different foods, such as sweet rowanberries (Grataegosorbus mitschurinii), common wheats (Triticum aestivum), nopals (Opuntia cochenillifera), grapefruits (Citrus X paradisi), and climbing beans (Vigna umbellata). This could make 1,3,5-trihydroxybenzene a potential biomarker for the consumption of these foods. 1,3,5-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. Based on a literature review a significant number of articles have been published on 1,3,5-Trihydroxybenzene.
Structure
Data?1676999880
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013675 (1,3,5-Trihydroxybenzene)

  Mrv1652309042000362D          

  9  9  0  0  0  0            999 V2000
    1.4294    1.2376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.8238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0007    1.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0007   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.0012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4294    1.2364    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0007   -1.2376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
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3D MOL for HMDB0013675 (1,3,5-Trihydroxybenzene)

HMDB0013675
     RDKit          3D
1,3,5-Trihydroxybenzene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.7060    2.6669    0.2655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3706    1.3203    0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523    0.3715   -0.0179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0538   -0.9847   -0.1116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0155   -1.9535   -0.3059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2698   -1.3388   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677   -0.3945    0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5812   -0.7982    0.2997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9558    0.9478    0.2858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0577    3.4027    0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3931    0.6860   -0.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4683   -2.3958    0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5222   -2.4061   -0.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1049   -0.8427   -0.5890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    1.7193    0.4399 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  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  2  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
  9 15  1  0
M  END
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3D SDF for HMDB0013675 (1,3,5-Trihydroxybenzene)

  Mrv1652309042000362D          

  9  9  0  0  0  0            999 V2000
    1.4294    1.2376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.8238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0007    1.2364    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0007   -0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -0.0012    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145    0.8238    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4294    1.2364    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0007   -1.2376    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  2  0  0  0  0
  3  7  2  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  5  9  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013675

> <DATABASE_NAME>
hmdb

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

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

> <INCHI_KEY>
QCDYQQDYXPDABM-UHFFFAOYSA-N

> <FORMULA>
C6H6O3

> <MOLECULAR_WEIGHT>
126.11

> <EXACT_MASS>
126.031694058

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
15

> <JCHEM_AVERAGE_POLARIZABILITY>
11.685180476962078

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
benzene-1,3,5-triol

> <ALOGPS_LOGP>
0.25

> <JCHEM_LOGP>
1.0625498509999998

> <ALOGPS_LOGS>
-0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
10.455560067223022

> <JCHEM_PKA_STRONGEST_ACIDIC>
9.126324331505472

> <JCHEM_PKA_STRONGEST_BASIC>
-5.370308771902201

> <JCHEM_POLAR_SURFACE_AREA>
60.69

> <JCHEM_REFRACTIVITY>
32.0007

> <JCHEM_ROTATABLE_BOND_COUNT>
0

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.58e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
phloroglucinol

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for HMDB0013675 (1,3,5-Trihydroxybenzene)

HMDB0013675
     RDKit          3D
1,3,5-Trihydroxybenzene
 15 15  0  0  0  0  0  0  0  0999 V2000
   -0.7060    2.6669    0.2655 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3706    1.3203    0.1767 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3523    0.3715   -0.0179 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0538   -0.9847   -0.1116 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0155   -1.9535   -0.3059 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2698   -1.3388   -0.0011 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2677   -0.3945    0.1949 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5812   -0.7982    0.2997 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9558    0.9478    0.2858 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0577    3.4027    0.4042 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3931    0.6860   -0.1015 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4683   -2.3958    0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5222   -2.4061   -0.0729 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1049   -0.8427   -0.5890 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7159    1.7193    0.4399 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  1  0
  4  6  2  0
  6  7  1  0
  7  8  1  0
  7  9  2  0
  9  2  1  0
  1 10  1  0
  3 11  1  0
  5 12  1  0
  6 13  1  0
  8 14  1  0
  9 15  1  0
M  END
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PDB for HMDB0013675 (1,3,5-Trihydroxybenzene)

HEADER    PROTEIN                                 04-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-SEP-20         0                                  
HETATM    1  O   UNK     0       2.668   2.310   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.334   1.538   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.001   2.308   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.334   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.001  -0.770   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.334  -0.002   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -1.334   1.538   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -2.668   2.308   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.001  -2.310   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4                                                  
CONECT    3    2    7                                                       
CONECT    4    2    5                                                       
CONECT    5    4    6    9                                                  
CONECT    6    5    7                                                       
CONECT    7    3    6    8                                                  
CONECT    8    7                                                            
CONECT    9    5                                                            
MASTER        0    0    0    0    0    0    0    0    9    0   18    0
END
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3D PDB for HMDB0013675 (1,3,5-Trihydroxybenzene)

COMPND    HMDB0013675
HETATM    1  O1  UNL     1      -0.706   2.667   0.265  1.00  0.00           O  
HETATM    2  C1  UNL     1      -0.371   1.320   0.177  1.00  0.00           C  
HETATM    3  C2  UNL     1      -1.352   0.371  -0.018  1.00  0.00           C  
HETATM    4  C3  UNL     1      -1.054  -0.985  -0.112  1.00  0.00           C  
HETATM    5  O2  UNL     1      -2.016  -1.953  -0.306  1.00  0.00           O  
HETATM    6  C4  UNL     1       0.270  -1.339  -0.001  1.00  0.00           C  
HETATM    7  C5  UNL     1       1.268  -0.394   0.195  1.00  0.00           C  
HETATM    8  O3  UNL     1       2.581  -0.798   0.300  1.00  0.00           O  
HETATM    9  C6  UNL     1       0.956   0.948   0.286  1.00  0.00           C  
HETATM   10  H1  UNL     1      -0.058   3.403   0.404  1.00  0.00           H  
HETATM   11  H2  UNL     1      -2.393   0.686  -0.101  1.00  0.00           H  
HETATM   12  H3  UNL     1      -2.468  -2.396   0.473  1.00  0.00           H  
HETATM   13  H4  UNL     1       0.522  -2.406  -0.073  1.00  0.00           H  
HETATM   14  H5  UNL     1       3.105  -0.843  -0.589  1.00  0.00           H  
HETATM   15  H6  UNL     1       1.716   1.719   0.440  1.00  0.00           H  
CONECT    1    2   10
CONECT    2    3    3    9
CONECT    3    4   11
CONECT    4    5    6    6
CONECT    5   12
CONECT    6    7   13
CONECT    7    8    9    9
CONECT    8   14
CONECT    9   15
END
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SMILES for HMDB0013675 (1,3,5-Trihydroxybenzene)

OC1=CC(O)=CC(O)=C1
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INCHI for HMDB0013675 (1,3,5-Trihydroxybenzene)

InChI=1S/C6H6O3/c7-4-1-5(8)3-6(9)2-4/h1-3,7-9H
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC6H6O3
Average Molecular Weight126.11
Monoisotopic Molecular Weight126.031694058
IUPAC Namebenzene-1,3,5-triol
Traditional Namephloroglucinol
CAS Registry Number108-73-6
SMILES
OC1=CC(O)=CC(O)=C1
InChI Identifier
InChI=1S/C6H6O3/c7-4-1-5(8)3-6(9)2-4/h1-3,7-9H
InChI KeyQCDYQQDYXPDABM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as phloroglucinols and derivatives. Phloroglucinols and derivatives are compounds containing a phloroglucinol (benzene-1,3,5-triol) moiety, which consists of a benzene ring bearing one hydroxyl group at positions 1,3, and 5.
KingdomOrganic compounds
Super ClassBenzenoids
ClassPhenols
Sub ClassBenzenetriols and derivatives
Direct ParentPhloroglucinols and derivatives
Alternative Parents
Substituents
  • Phloroglucinol derivative
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Monocyclic benzene moiety
  • Polyol
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aromatic homomonocyclic compound
Molecular FrameworkAromatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
Role
Industrial applicationBiological role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point218.5 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility10.6 mg/mL at 20 °CNot Available
LogP0.16Not Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Feces
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Male
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedNot SpecifiedNot Specified
Normal		 details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDDB12944
Phenol Explorer Compound ID658
FooDB IDFDB013879
KNApSAcK IDC00002665
Chemspider ID352
KEGG Compound IDC02183
BioCyc IDCPD-16
BiGG IDNot Available
Wikipedia LinkPhloroglucinol
METLIN IDNot Available
PubChem Compound359
PDB IDNot Available
ChEBI ID16204
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Achkar J, Xian M, Zhao H, Frost JW: Biosynthesis of phloroglucinol. J Am Chem Soc. 2005 Apr 20;127(15):5332-3. doi: 10.1021/ja042340g. [PubMed:15826166 ]