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Ubiquinone-6 (YMDB00660)

Identification
YMDB IDYMDB00660
NameUbiquinone-6
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionUbiquinone 6 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). Based on a literature review a significant number of articles have been published on Ubiquinone 6.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • (all-E)-2-(3,7,11,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaenyl)-5,6-dimethoxy-3-methyl-2,5-cyclohexadiene-1,4-dione
  • 2,3-dimethoxy-5-methyl-6-hexaprenyl-1,4-benzoquinone
  • Coenzyme Q6
  • Coenzyme Qq6
  • CoQ6
  • Ubiquinone 30
  • Ubiquinone 6
  • Ubiquinone Q6
  • Coenzyme-Q6
  • CoQ-6
  • Ubiquinone(6)
  • UBIQUINONE-6
CAS number1065-31-2
WeightAverage: 590.8754
Monoisotopic: 590.433510344
InChI KeyGXNFPEOUKFOTKY-LPHQIWJTSA-N
InChIInChI=1S/C39H58O4/c1-28(2)16-11-17-29(3)18-12-19-30(4)20-13-21-31(5)22-14-23-32(6)24-15-25-33(7)26-27-35-34(8)36(40)38(42-9)39(43-10)37(35)41/h16,18,20,22,24,26H,11-15,17,19,21,23,25,27H2,1-10H3/b29-18+,30-20+,31-22+,32-24+,33-26+
IUPAC Name2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Traditional IUPAC Name2-(3,7,11,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaen-1-yl)-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione
Chemical FormulaC39H58O4
SMILESCOC1=C(OC)C(=O)C(C\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CC\C=C(/C)CCC=C(C)C)=C(C)C1=O
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
  • Polyprenylbenzoquinone
  • Sesterterpenoid
  • Ubiquinone skeleton
  • Quinone
  • P-benzoquinone
  • Vinylogous ester
  • Cyclic ketone
  • Ketone
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External Descriptors
Physical Properties
StateLiquid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.00032 g/LALOGPS
logP8.41ALOGPS
logP10.52ChemAxon
logS-6.3ALOGPS
pKa (Strongest Basic)-4.7ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area52.6 ŲChemAxon
Rotatable Bond Count19ChemAxon
Refractivity191.39 m³·mol⁻¹ChemAxon
Polarizability73.45 ųChemAxon
Number of Rings1ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • mitochondrion
Organoleptic PropertiesNot Available
SMPDB Pathways
Ubiquinone BiosynthesisPW002473 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Ubiquinone and other terpenoid-quinone biosynthesisec00130 Map00130
SMPDB ReactionsNot Available
KEGG Reactions
Spermidine + Ubiquinone-6 + water → 1,3-Diaminopropane + Ubiquinol-6 + 4-aminobutanal
Ubiquinone-6 + L-Dihydroorotic acid → Ubiquinol-6 + Orotic acid
Ubiquinol-6 + hydron + ferricytochrome c → ferrocytochrome c + Ubiquinone-6 + hydron
Ubiquinone-6 + Formic acid + hydron → Ubiquinol-6 + Carbon dioxide
NADH + Ubiquinone-6 + hydron → NAD + Ubiquinol-6
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0fi9-2268490000-d4a46fb7bbfe567b3bc9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0007-0112190000-0e3f9b8afdf1ec72101dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002b-0649330000-25374eb6b7e2528209f9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00kb-2125910000-2353dc21b36ad0226438JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0000090000-888a7e1c1887cd6289a7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0000090000-cdb5f8e03d488aabf72fJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0079-9100580000-0ddcd7334398c6806be9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0007-0212190000-d6790c276a238e59aecaJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-002b-0649330000-25374eb6b7e2528209f9JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00mk-2125910000-fd96f37265811c6c3531JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0000090000-1e48e9465d0a2b5e046cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-000i-0100090000-308b58d9d2d89e2a0150JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0079-8100590000-fa8ea854e31b895398f6JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-000e-4619380000-15b4ea76379fc8709a54JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-4915010000-9f9f91ee19707f8366d2JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000y-8924000000-472232f8797340057410JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000i-0000090000-652b47e044f4b53fb940JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-07br-0611090000-96454b02ed13c80d5269JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-003r-1694370000-5e9b03bff5e8c4cb6b63JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Sippel, C. J., Goewert, R. R., Slachman, F. N., Olson, R. E. (1983). "The regulation of ubiquinone-6 biosynthesis by Saccharomyces cerevisiae." J Biol Chem 258:1057-1061.6296069
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID52971
HMDB IDHMDB0036062
Pubchem Compound ID5283544
Kegg IDC17568
ChemSpider ID23354078
FOODB IDFDB014886
Wikipedia IDNot Available
BioCyc IDNot Available

Enzymes

Protein Details
1. Deoxyhypusine synthase
General function:
Involved in peptidyl-lysine modification to hypusine
Specific function:
Catalyzes the NAD-dependent oxidative cleavage of spermidine and the subsequent transfer of the butylamine moiety of spermidine to the epsilon-amino group of a specific lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue
Gene Name:
DYS1
Uniprot ID:
P38791
Molecular weight:
42891.80078
Reactions
[eIF5A-precursor]-lysine + spermidine → [eIF5A-precursor]-deoxyhypusine + propane-1,3-diamine.
Protein Details
2. External NADH-ubiquinone oxidoreductase 2, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
External NADH dehydrogenase required for optimum cellular growth with a number of nonfermentable carbon sources, including ethanol. With NDE1, performes the mitochondrial oxidation of cytosolic NADH under these growth conditions. Regulates the mitochondrial glycerol-3-phosphate dehydrogenase, GUT2, also involved in cytosolic NADH oxydation
Gene Name:
NDE2
Uniprot ID:
Q07500
Molecular weight:
61658.69922
Reactions
NADH + ubiquinone → NAD(+) + ubiquinol.
Protein Details
3. External NADH-ubiquinone oxidoreductase 1, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
External NADH dehydrogenase required for optimum cellular growth with a number of nonfermentable carbon sources, including ethanol. With NDE2, performes the mitochondrial oxidation of cytosolic NADH under these growth conditions. Regulates the mitochondrial glycerol-3-phosphate dehydrogenase, GUT2, also involved in cytosolic NADH oxydation
Gene Name:
NDE1
Uniprot ID:
P40215
Molecular weight:
62773.60156
Reactions
NADH + ubiquinone → NAD(+) + ubiquinol.
Protein Details
4. Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
General function:
Involved in oxidoreductase activity
Specific function:
Catalyzes the oxidation of NADH generated inside the Mitochondrion
Gene Name:
NDI1
Uniprot ID:
P32340
Molecular weight:
57249.30078
Reactions
NADH + ubiquinone → NAD(+) + ubiquinol.
Protein Details
5. Succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial
General function:
Involved in 2 iron, 2 sulfur cluster binding
Specific function:
Subunit of succinate dehydrogenase (SDH) that is involved in complex II of the mitochondrial electron transport chain and is responsible for transferring electrons from succinate to ubiquinone (coenzyme Q). SDH1 and SDH2 form the catalytic dimer. Electrons flow from succinate to the FAD bound to SDH1, and sequentially through the iron-sulfur clusters bound to SDH2 and enter the membrane dimer formed by SDH3 and SDH4
Gene Name:
SDH2
Uniprot ID:
P21801
Molecular weight:
30230.90039
Reactions
Succinate + ubiquinone → fumarate + ubiquinol.
Protein Details
6. Dihydroorotate dehydrogenase
General function:
Involved in catalytic activity
Specific function:
In the de novo pyrimidine biosynthesic pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate and the reduction of fumarate to succinate. Does not use oxaloacetate and NAD or NADP as electron acceptors
Gene Name:
URA1
Uniprot ID:
P28272
Molecular weight:
34800.60156
Reactions
(S)-dihydroorotate + O(2) → orotate + H(2)O(2).
(S)-dihydroorotate + a quinone → orotate + a quinol
Protein Details
7. Cytochrome c iso-1
General function:
Involved in iron ion binding
Specific function:
Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain
Gene Name:
CYC1
Uniprot ID:
P00044
Molecular weight:
12181.90039
Reactions
Protein Details
8. Cytochrome c iso-2
General function:
Involved in iron ion binding
Specific function:
Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain
Gene Name:
CYC7
Uniprot ID:
P00045
Molecular weight:
12532.2998
Reactions