5-Methylaminomethyl-2-selenouridine (ECMDB20237) (M2MDB001080)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-05-31 14:34:37 -0600
Update Date2015-06-03 17:19:36 -0600
Secondary Accession Numbers
  • ECMDB20237
Identification
Name:5-Methylaminomethyl-2-selenouridine
Description5-methylaminomethyl-2-selenouridine is a member of the chemical class known as Pyrimidine Nucleosides and Analogues. These are compounds comprising a pyrimidine base attached to a sugar. 5-methylaminomethyl-2-selenouridine is invovled in Selenouridine biosynthesis (tRNA).
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5-((Methylamino)methyl)-2-seleno-Uridine
  • 5-((Methylamino)methyl)-2-selenouridine
  • 5-Mamsu
  • Mnm(5)se(2)U
Chemical Formula:C11H17N3O5Se
Weight:Average: 350.23
Monoisotopic: 351.033342497
InChI Key:LKYNRXHIWDCZMH-GHCJXIJMSA-N
InChI:InChI=1S/C11H17N3O5Se/c1-12-2-5-3-14(11(20)13-9(5)18)10-8(17)7(16)6(4-15)19-10/h3,6-8,10,12,15-17H,2,4H2,1H3,(H,13,18,20)/t6-,7-,8-,10-/m0/s1
CAS number:89314-80-7
IUPAC Name:1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]-1,2-dihydropyrimidine-2-selone
Traditional IUPAC Name:1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]pyrimidine-2-selone
SMILES:[H][C@@]1(CO)O[C@]([H])(N2C=C(CNC)C(O)=NC2=[Se])[C@@]([H])(O)[C@@]1([H])O
Chemical Taxonomy
Description belongs to the class of organic compounds known as pyrimidine nucleosides. Pyrimidine nucleosides are compounds comprising a pyrimidine base attached to a ribosyl or deoxyribosyl moiety.
KingdomOrganic compounds
Super ClassNucleosides, nucleotides, and analogues
ClassPyrimidine nucleosides
Sub ClassNot Available
Direct ParentPyrimidine nucleosides
Alternative Parents
Substituents
  • Pyrimidine nucleoside
  • N-glycosyl compound
  • Glycosyl compound
  • Pentose monosaccharide
  • Hydroxypyrimidine
  • Aralkylamine
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Tetrahydrofuran
  • Secondary alcohol
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Organoselenium compound
  • Organooxygen compound
  • Organonitrogen compound
  • Amine
  • Alcohol
  • Aromatic heteromonocyclic compound
Molecular FrameworkAromatic heteromonocyclic compounds
External DescriptorsNot Available
Physical Properties
State:Not Available
Charge:1
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility146 g/LALOGPS
logP-1.8ALOGPS
logP-2.8ChemAxon
logS-0.38ALOGPS
pKa (Strongest Acidic)7.37ChemAxon
pKa (Strongest Basic)9.2ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area117.78 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity77.72 m³·mol⁻¹ChemAxon
Polarizability28.74 ųChemAxon
Number of Rings2ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
5-Methylaminomethyl-2-thiouridine + Phosphoroselenoic acid > 5-Methylaminomethyl-2-selenouridine + Inorganic phosphate
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
EcoCyc Pathways:Not Available
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_4_5) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-0049000000-018fac8800b968dfb504View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0gb9-0191000000-3137c1da62b0fa35cd3fView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0gdi-3890000000-0a91496f8685a82e5d6bView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0uxr-2295000000-f614b01c36dcca13dffeView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-014i-3192000000-714a02347a0a7cd600b5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-066s-3960000000-413abf7a2f319169a76fView in MoNA
MSMass Spectrum (Electron Ionization)Not AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI IDNot Available
HMDB IDNot Available
Pubchem Compound ID6336326
Kegg IDNot Available
ChemSpider ID4891617
Wikipedia IDNot Available
BioCyc ID5-METHYLAMINOMETHYL-2-SELENOURIDINE
EcoCyc ID5-METHYLAMINOMETHYL-2-SELENOURIDINE

Enzymes

Protein Details
1. tRNA 2-selenouridine synthase
General function:
Involved in transferase activity, transferring selenium-containing groups
Specific function:
Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
Gene Name:
selU
Uniprot ID:
P33667
Molecular weight:
41110
Reactions
5-methylaminomethyl-2-thiouridine + selenophosphate = 5-methylaminomethyl-2-selenouridine + phosphate.