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Showing metabocard for 2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol (HMDB0132663)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (2) Show 2 proteinsXML
enzymes (2) Show 2 proteins
Record Information
Version4.0
StatusPredicted
Creation Date2017-09-17 17:00:13 UTC
Update Date2019-11-12 17:22:29 UTC
HMDB IDHMDB0132663
Secondary Accession NumbersNone
Metabolite Identification
Common Name2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol
Description2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose. 2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol is a predicted metabolite generated by BioTransformer¹ that is produced by the metabolism of 3-(3,4-dihydroxyphenyl)-1-{2,4,6-trihydroxy-3-phenyl}propan-1-one. 2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol is an extremely weak basic (essentially neutral) compound (based on its pKa). This keto-hydrolysis-pattern5 occurs in humans and human gut microbiota. It is generated by EC.3.7.1.and unspecified-gutmicro enzymes via a keto-hydrolysis-pattern5 reaction.
Structure
Data?1563875950
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
SynonymsNot Available
Chemical FormulaC12H16O8
Average Molecular Weight288.252
Monoisotopic Molecular Weight288.084517475
IUPAC Name2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol
Traditional Name2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol
CAS Registry NumberNot Available
SMILES
OCC1OC(C(O)C(O)C1O)C1=C(O)C=C(O)C=C1O
InChI Identifier
InChI=1S/C12H16O8/c13-3-7-9(17)10(18)11(19)12(20-7)8-5(15)1-4(14)2-6(8)16/h1-2,7,9-19H,3H2
InChI KeyWHDIYCULVGAWGN-UHFFFAOYSA-N
Chemical Taxonomy
Description belongs to the class of organic compounds known as phenolic glycosides. These are organic compounds containing a phenolic structure attached to a glycosyl moiety. Some examples of phenolic structures include lignans, and flavonoids. Among the sugar units found in natural glycosides are D-glucose, L-Fructose, and L rhamnose.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPhenolic glycosides
Alternative Parents
Substituents
  • Phenolic glycoside
  • C-glycosyl compound
  • Benzenetriol
  • Phloroglucinol derivative
  • 1-hydroxy-4-unsubstituted benzenoid
  • 1-hydroxy-2-unsubstituted benzenoid
  • Phenol
  • Monocyclic benzene moiety
  • Benzenoid
  • Monosaccharide
  • Oxane
  • Secondary alcohol
  • Oxacycle
  • Organoheterocyclic compound
  • Dialkyl ether
  • Ether
  • Polyol
  • Hydrocarbon derivative
  • Alcohol
  • Primary alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Ontology
Disposition

Source:

Physical Properties
StateNot Available
Experimental Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Predicted Properties
PropertyValueSource
logP-1.5ALOGPS
logP-1.7ChemAxon
logS-0.74ALOGPS
pKa (Strongest Acidic)8.77ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count8ChemAxon
Hydrogen Donor Count7ChemAxon
Polar Surface Area150.84 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity65.12 m³·mol⁻¹ChemAxon
Polarizability26.95 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityYesChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (5 TMS) - 70eV, Positivesplash10-00m0-2505967000-1e8c49b3e0a1a2c2d88aSpectrum
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0079-3940000000-b788d54d2595ca87949cSpectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000i-0090000000-eb81a3cb2d4279972ad3Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0079-4790000000-c0871c0d276532ad8c15Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0udr-3900000000-43aff77696b6d1b80570Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0290000000-cb70f1bd6e9f4ceadc19Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-0170-4960000000-224bafd314f928414e88Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-056u-8900000000-03e8d83ed3f829e94038Spectrum
Biological Properties
Cellular LocationsNot Available
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound86246098
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Djoumbou Feunang, Yannick (2017). Cheminformatics Tools for Enabling Metabolomics, 2017 (PhD thesis). University of Alberta.

Enzymes

Enzyme Details
1. Sulfotransferase family cytosolic 2B member 1
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 many hormones, neurotransmitters, drugs and xenobiotic compounds. Sulfonation increases the water solubility of most compounds, and therefore their renal excretion, but it can also result in bioactivation to form active metabolites. Sulfates hydroxysteroids like DHEA. Isoform 1 preferentially sulfonates cholesterol, and isoform 2 avidly sulfonates pregnenolone but not cholesterol.
Gene Name:
SULT2B1
Uniprot ID:
O00204
Molecular weight:
39598.595
Reactions
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → {[3,4,5-trihydroxy-6-(2,4,6-trihydroxyphenyl)oxan-2-yl]methoxy}sulfonic aciddetails
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → [4,5-dihydroxy-2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxan-3-yl]oxidanesulfonic aciddetails
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → [3,5-dihydroxy-2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxan-4-yl]oxidanesulfonic aciddetails
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → [4,5-dihydroxy-6-(hydroxymethyl)-2-(2,4,6-trihydroxyphenyl)oxan-3-yl]oxidanesulfonic aciddetails
Enzyme Details
2. 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
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → 6-{3,5-dihydroxy-2-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic aciddetails
2-(hydroxymethyl)-6-(2,4,6-trihydroxyphenyl)oxane-3,4,5-triol → 6-{3,5-dihydroxy-4-[3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]phenoxy}-3,4,5-trihydroxyoxane-2-carboxylic aciddetails