Hmdb loader
Survey
You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database.
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2013-05-17 00:56:14 UTC
Update Date2021-09-14 14:57:44 UTC
HMDB IDHMDB0060359
Secondary Accession Numbers
  • HMDB60359
Metabolite Identification
Common Name2,3-Epoxymenaquinone
Description2,3-Epoxymenaquinone, also known as vitamin K2 2,3-epoxide, belongs to the class of organic compounds known as menaquinones. These are vitamin K2 compounds consisting of a naphtho-1,4-quinone ring system, which is substituted at the 2-position by an isoprenyl side-chain, and usually, at the 3-position by a methyl group. 2,3-Epoxymenaquinone is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563866049
Synonyms
ValueSource
Vitamin K2 2,3-epoxideKegg
Vitamin K2-2,3-epoxideHMDB
Chemical FormulaC21H24O3
Average Molecular Weight324.4135
Monoisotopic Molecular Weight324.172544634
IUPAC Name1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methyl-1aH,2H,7H,7aH-naphtho[2,3-b]oxirene-2,7-dione
Traditional Name1a-[(2E)-3,7-dimethylocta-2,6-dien-1-yl]-7a-methylnaphtho[2,3-b]oxirene-2,7-dione
CAS Registry NumberNot Available
SMILES
CC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O
InChI Identifier
InChI=1S/C21H24O3/c1-14(2)8-7-9-15(3)12-13-21-19(23)17-11-6-5-10-16(17)18(22)20(21,4)24-21/h5-6,8,10-12H,7,9,13H2,1-4H3/b15-12+
InChI KeyZEACJJRPAPKYKW-NTCAYCPXSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as menaquinones. These are vitamin K2 compounds consisting of a naphtho-1,4-quinone ring system, which is substituted at the 2-position by an isoprenyl side-chain, and usually, at the 3-position by a methyl group.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassQuinone and hydroquinone lipids
Direct ParentMenaquinones
Alternative Parents
Substituents
  • Menaquinone
  • Naphthoquinone
  • Aromatic monoterpenoid
  • Monoterpenoid
  • Naphthalene
  • Tetralin
  • Quinone
  • Aryl alkyl ketone
  • Aryl ketone
  • Benzenoid
  • Ketone
  • Oxacycle
  • Ether
  • Oxirane
  • Dialkyl ether
  • Organoheterocyclic compound
  • Organooxygen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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 Solubility0.0056 g/LALOGPS
logP4.44ALOGPS
logP4.69ChemAxon
logS-4.8ALOGPS
pKa (Strongest Basic)-4.4ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count3ChemAxon
Hydrogen Donor Count0ChemAxon
Polar Surface Area46.67 ŲChemAxon
Rotatable Bond Count5ChemAxon
Refractivity96.63 m³·mol⁻¹ChemAxon
Polarizability36.6 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+179.62531661259
DarkChem[M-H]-174.8531661259
DeepCCS[M-2H]-208.76230932474
DeepCCS[M+Na]+184.15830932474
AllCCS[M+H]+181.032859911
AllCCS[M+H-H2O]+177.932859911
AllCCS[M+NH4]+183.932859911
AllCCS[M+Na]+184.832859911
AllCCS[M-H]-186.832859911
AllCCS[M+Na-2H]-186.932859911
AllCCS[M+HCOO]-187.132859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
2,3-EpoxymenaquinoneCC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O3374.7Standard polar33892256
2,3-EpoxymenaquinoneCC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O2440.0Standard non polar33892256
2,3-EpoxymenaquinoneCC(C)=CCC\C(C)=C\CC12OC1(C)C(=O)C1=CC=CC=C1C2=O2428.6Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Epoxymenaquinone GC-MS (Non-derivatized) - 70eV, Positivesplash10-0lk9-8943000000-09988d4900b0f59534bc2017-09-20Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Epoxymenaquinone GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - 2,3-Epoxymenaquinone 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 - 2,3-Epoxymenaquinone 10V, Positive-QTOFsplash10-004i-0129000000-6c020f5170781e25b0ba2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 20V, Positive-QTOFsplash10-0lmi-8983000000-f9a13cf6b46481ecf36a2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 40V, Positive-QTOFsplash10-0aor-9310000000-4475f464c265ee73e5cd2017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 10V, Negative-QTOFsplash10-00di-0009000000-ed9620dbea687e569cc02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 20V, Negative-QTOFsplash10-00di-0119000000-8c113c8b5fd7944b6be02017-10-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 2,3-Epoxymenaquinone 40V, Negative-QTOFsplash10-1000-5962000000-8170859910f9c08c34d72017-10-06Wishart 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 IDC20265
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound71448979
PDB IDNot Available
ChEBI IDNot Available
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 gamma-glutamyl carboxylase activity
Specific function:
Mediates the vitamin K-dependent carboxylation of glutamate residues to calcium-binding gamma-carboxyglutamate (Gla) residues with the concomitant conversion of the reduced hydroquinone form of vitamin K to vitamin K epoxide.
Gene Name:
GGCX
Uniprot ID:
P38435
Molecular weight:
87560.065
Reactions
2,3-Epoxymenaquinone + Gla protein + Water → Menaquinol + Gla protein precursor + Carbon dioxide + Oxygendetails
General function:
Involved in vitamin-K-epoxide reductase (warfarin-sensi
Specific function:
Involved in vitamin K metabolism. Catalytic subunit of the vitamin K epoxide reductase (VKOR) complex which reduces inactive vitamin K 2,3-epoxide to active vitamin K.
Gene Name:
VKORC1
Uniprot ID:
Q9BQB6
Molecular weight:
18234.3
Reactions
2,3-Epoxymenaquinone + 1,4-Dithiothreitol → Menatetrenone + Oxidized dithiothreitol + Waterdetails