Hmdb loader
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:01:08 UTC
Update Date2022-03-07 02:53:39 UTC
HMDB IDHMDB0033304
Secondary Accession Numbers
  • HMDB33304
Metabolite Identification
Common NameGerberinol
DescriptionGerberinol belongs to the class of organic compounds known as 4-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to C4-position the coumarin skeleton. Gerberinol has been detected, but not quantified in, fruits. This could make gerberinol a potential biomarker for the consumption of these foods. Based on a literature review very few articles have been published on Gerberinol.
Structure
Data?1563862384
Synonyms
ValueSource
3,3'-Methylenebis[4-hydroxy-5-methyl-2H-1-benzopyran-2-one], 9ciHMDB
Chemical FormulaC21H16O6
Average Molecular Weight364.3481
Monoisotopic Molecular Weight364.094688244
IUPAC Name4-hydroxy-3-[(4-hydroxy-5-methyl-2-oxo-2H-chromen-3-yl)methyl]-5-methyl-2H-chromen-2-one
Traditional Name4-hydroxy-3-[(4-hydroxy-5-methyl-2-oxochromen-3-yl)methyl]-5-methylchromen-2-one
CAS Registry Number84153-78-6
SMILES
CC1=C2C(O)=C(CC3=C(O)C4=C(C)C=CC=C4OC3=O)C(=O)OC2=CC=C1
InChI Identifier
InChI=1S/C21H16O6/c1-10-5-3-7-14-16(10)18(22)12(20(24)26-14)9-13-19(23)17-11(2)6-4-8-15(17)27-21(13)25/h3-8,22-23H,9H2,1-2H3
InChI KeyJUCUEMBIORWHSB-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 4-hydroxycoumarins. These are coumarins that contain one or more hydroxyl groups attached to C4-position the coumarin skeleton.
KingdomOrganic compounds
Super ClassPhenylpropanoids and polyketides
ClassCoumarins and derivatives
Sub ClassHydroxycoumarins
Direct Parent4-hydroxycoumarins
Alternative Parents
Substituents
  • 4-hydroxycoumarin
  • Benzopyran
  • 1-benzopyran
  • Pyranone
  • Pyran
  • Benzenoid
  • Heteroaromatic compound
  • Vinylogous acid
  • Lactone
  • Oxacycle
  • Organoheterocyclic compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
Role
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting Point267 - 269 °CNot Available
Boiling PointNot AvailableNot Available
Water Solubility13.42 mg/L @ 25 °C (est)The Good Scents Company Information System
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.026 g/LALOGPS
logP2.41ALOGPS
logP-0.57ChemAxon
logS-4.2ALOGPS
pKa (Strongest Acidic)-12ChemAxon
pKa (Strongest Basic)-3.1ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count2ChemAxon
Polar Surface Area93.06 ŲChemAxon
Rotatable Bond Count2ChemAxon
Refractivity99.28 m³·mol⁻¹ChemAxon
Polarizability36.36 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+184.04731661259
DarkChem[M-H]-181.58931661259
DeepCCS[M+H]+185.53430932474
DeepCCS[M-H]-183.17630932474
DeepCCS[M-2H]-217.15830932474
DeepCCS[M+Na]+192.37330932474
AllCCS[M+H]+186.232859911
AllCCS[M+H-H2O]+183.032859911
AllCCS[M+NH4]+189.332859911
AllCCS[M+Na]+190.132859911
AllCCS[M-H]-183.532859911
AllCCS[M+Na-2H]-182.632859911
AllCCS[M+HCOO]-181.732859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
GerberinolCC1=C2C(O)=C(CC3=C(O)C4=C(C)C=CC=C4OC3=O)C(=O)OC2=CC=C14587.0Standard polar33892256
GerberinolCC1=C2C(O)=C(CC3=C(O)C4=C(C)C=CC=C4OC3=O)C(=O)OC2=CC=C12897.7Standard non polar33892256
GerberinolCC1=C2C(O)=C(CC3=C(O)C4=C(C)C=CC=C4OC3=O)C(=O)OC2=CC=C13433.4Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Gerberinol,1TMS,isomer #1CC1=CC=CC2=C1C(O)=C(CC1=C(O[Si](C)(C)C)C3=C(C)C=CC=C3OC1=O)C(=O)O23359.7Semi standard non polar33892256
Gerberinol,2TMS,isomer #1CC1=CC=CC2=C1C(O[Si](C)(C)C)=C(CC1=C(O[Si](C)(C)C)C3=C(C)C=CC=C3OC1=O)C(=O)O23301.7Semi standard non polar33892256
Gerberinol,1TBDMS,isomer #1CC1=CC=CC2=C1C(O)=C(CC1=C(O[Si](C)(C)C(C)(C)C)C3=C(C)C=CC=C3OC1=O)C(=O)O23585.5Semi standard non polar33892256
Gerberinol,2TBDMS,isomer #1CC1=CC=CC2=C1C(O[Si](C)(C)C(C)(C)C)=C(CC1=C(O[Si](C)(C)C(C)(C)C)C3=C(C)C=CC=C3OC1=O)C(=O)O23801.2Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Gerberinol GC-MS (Non-derivatized) - 70eV, Positivesplash10-0079-0409000000-297bb17bc79ed3cb42682017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gerberinol GC-MS (2 TMS) - 70eV, Positivesplash10-0596-3520900000-32bb4b5dd042df0224702017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Gerberinol GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 10V, Positive-QTOFsplash10-014i-0109000000-47ea59f0bbe442e7ed122016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 20V, Positive-QTOFsplash10-014r-0709000000-b89f2d986412211a96f12016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 40V, Positive-QTOFsplash10-00kr-2911000000-0dec0fc632ac9fa227ef2016-08-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 10V, Negative-QTOFsplash10-03di-0109000000-7ef6a203edfe0495570f2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 20V, Negative-QTOFsplash10-004i-0905000000-53eded26ddcef79eba9b2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 40V, Negative-QTOFsplash10-014i-2912000000-284cfe20c13a701760cf2016-08-03Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 10V, Positive-QTOFsplash10-014i-0009000000-cae28d8ce1701ad1ef1c2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 20V, Positive-QTOFsplash10-0170-0809000000-aabadae31d1a0ed018302021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 40V, Positive-QTOFsplash10-0006-8595000000-41102c906841c9dfdacf2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 10V, Negative-QTOFsplash10-03di-0009000000-5f2291b852f2272a99e22021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 20V, Negative-QTOFsplash10-03di-0109000000-27b8bb3b6c64ae4510662021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Gerberinol 40V, Negative-QTOFsplash10-052r-0921000000-ccfff7728936d3a1917f2021-09-24Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB011328
KNApSAcK IDC00050595
Chemspider ID30776991
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound54714260
PDB IDNot Available
ChEBI ID172592
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1834621
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

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
Gerberinol → 3,4,5-trihydroxy-6-({3-[(4-hydroxy-5-methyl-2-oxo-2H-chromen-3-yl)methyl]-5-methyl-2-oxo-2H-chromen-4-yl}oxy)oxane-2-carboxylic aciddetails