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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:56:59 UTC
Update Date2022-03-07 03:17:44 UTC
HMDB IDHMDB0060370
Secondary Accession Numbers
  • HMDB60370
Metabolite Identification
Common Name3-Demethylubiquinone-9
Description3-Demethylubiquinone-9 belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6). Thus, 3-demethylubiquinone-9 is considered to be a quinone lipid molecule. 3-Demethylubiquinone-9 is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Data?1563866051
SynonymsNot Available
Chemical FormulaC53H80O4
Average Molecular Weight781.1999
Monoisotopic Molecular Weight780.605661048
IUPAC Name2-hydroxy-3-methoxy-6-methyl-5-[(2E,6E,10E,14E,18E,22E,26E,30E)-3,7,11,15,19,23,27,31,35-nonamethylhexatriaconta-2,6,10,14,18,22,26,30,34-nonaen-1-yl]cyclohexa-2,5-diene-1,4-dione
Traditional Name3-demethylubiquinone-9
CAS Registry NumberNot Available
SMILES
COC1=C(O)C(=O)C(C)=C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)C1=O
InChI Identifier
InChI=1S/C53H80O4/c1-39(2)21-13-22-40(3)23-14-24-41(4)25-15-26-42(5)27-16-28-43(6)29-17-30-44(7)31-18-32-45(8)33-19-34-46(9)35-20-36-47(10)37-38-49-48(11)50(54)52(56)53(57-12)51(49)55/h21,23,25,27,29,31,33,35,37,56H,13-20,22,24,26,28,30,32,34,36,38H2,1-12H3/b40-23+,41-25+,42-27+,43-29+,44-31+,45-33+,46-35+,47-37+
InChI KeyYFPCPZJYSKOLNK-NSCWJZNLSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as ubiquinones. These are coenzyme Q derivatives containing a 5, 6-dimethoxy-3-methyl(1,4-benzoquinone) moiety to which an isoprenyl group is attached at ring position 2(or 6).
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassQuinone and hydroquinone lipids
Direct ParentUbiquinones
Alternative Parents
Substituents
  • Polyterpenoid
  • Polyprenylbenzoquinone
  • Ubiquinone skeleton
  • Quinone
  • P-benzoquinone
  • Vinylogous ester
  • Vinylogous acid
  • Cyclic ketone
  • Ketone
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Ontology
Physiological effectNot Available
Disposition
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.00024 g/LALOGPS
logP9.8ALOGPS
logP15.38ChemAxon
logS-6.5ALOGPS
pKa (Strongest Acidic)8.31ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area63.6 ŲChemAxon
Rotatable Bond Count27ChemAxon
Refractivity258.05 m³·mol⁻¹ChemAxon
Polarizability100.07 ųChemAxon
Number of Rings1ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+296.18830932474
DeepCCS[M-H]-294.29330932474
DeepCCS[M-2H]-328.0730932474
DeepCCS[M+Na]+302.18530932474
AllCCS[M+H]+294.832859911
AllCCS[M+H-H2O]+294.232859911
AllCCS[M+NH4]+295.332859911
AllCCS[M+Na]+295.432859911
AllCCS[M-H]-251.032859911
AllCCS[M+Na-2H]-255.232859911
AllCCS[M+HCOO]-259.932859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
3-Demethylubiquinone-9COC1=C(O)C(=O)C(C)=C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)C1=O6335.3Standard polar33892256
3-Demethylubiquinone-9COC1=C(O)C(=O)C(C)=C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)C1=O4699.3Standard non polar33892256
3-Demethylubiquinone-9COC1=C(O)C(=O)C(C)=C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)C1=O5268.5Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 3-Demethylubiquinone-9 GC-MS (Non-derivatized) - 70eV, Positivesplash10-014r-1187643900-661c5bbeacf3ea1bef342017-11-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Demethylubiquinone-9 GC-MS (TMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 3-Demethylubiquinone-9 GC-MS (TBDMS_1_1) - 70eV, PositiveNot Available2021-10-18Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 10V, Positive-QTOFsplash10-001i-0212121900-80fa4524bf6aa92464ac2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 20V, Positive-QTOFsplash10-01rt-1556392300-42347057fe3319c0e6592017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 40V, Positive-QTOFsplash10-0092-1111239100-45d69d34e737c896605f2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 10V, Negative-QTOFsplash10-004i-0000000900-4cd2b0042c79d14e406f2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 20V, Negative-QTOFsplash10-004i-0000003900-6fae04f9417fe1d622d72017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 40V, Negative-QTOFsplash10-0nor-3100009600-c041aaab68db775f4ba02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 10V, Positive-QTOFsplash10-001i-3110324900-5fbf9c6c4586c5ac11692021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 20V, Positive-QTOFsplash10-0ff0-9636818500-5a4cdb2c1675dd4753202021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 40V, Positive-QTOFsplash10-0036-9613510000-a902aff6900205f78ffb2021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 10V, Negative-QTOFsplash10-004i-0000000900-54f09126de3eb0ec46772021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 20V, Negative-QTOFsplash10-004j-0300002900-ea0cd0290b7061a748d92021-10-12Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 3-Demethylubiquinone-9 40V, Negative-QTOFsplash10-0j6u-1890213200-690fc9c7f679cfa61fd32021-10-12Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Membrane (predicted from logP)
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 IDC03226
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound135398691
PDB IDNot Available
ChEBI ID18238
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. Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]
  2. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  3. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  4. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  5. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

General function:
Involved in methyltransferase activity
Specific function:
Not Available
Gene Name:
COQ3
Uniprot ID:
Q9NZJ6
Molecular weight:
41053.76
Reactions
S-Adenosylmethionine + 3-Demethylubiquinone-9 → S-Adenosylhomocysteine + Coenzyme Q9details