5-Methylaminomethyl-2-thiouridine (ECMDB20238) (M2MDB001081)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes (1)XML
Proteins (1)
Record Information
Version2.0
Creation Date2012-05-31 14:34:40 -0600
Update Date2015-06-03 17:19:36 -0600
Secondary Accession Numbers
  • ECMDB20238
Identification
Name:5-Methylaminomethyl-2-thiouridine
Description5-methylaminomethyl-2-thiouridine 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-thiouridine is invovled in Selenouridine biosynthesis (tRNA). The selenium-modified nucleoside is 5-methyl-aminomethyl-2-selenouridine (mnm5Se2U), which is the chemical analog of 5-methylaminomethyl-2-thiouridine, a previously identified minor base of E. coli. tRNA2Glu. (PMID 6227514)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 2-Thio-5-methylaminomethyluridine
  • 5-((Methylamino)methyl)-2-thio-Uridine
Chemical Formula:C11H17N3O5S
Weight:Average: 303.335
Monoisotopic: 303.088891359
InChI Key:HXVKEKIORVUWDR-GHCJXIJMSA-N
InChI:InChI=1S/C11H17N3O5S/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:32860-54-1
IUPAC Name:1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]-1,2-dihydropyrimidine-2-thione
Traditional IUPAC Name:1-[(2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-5-[(methylamino)methyl]pyrimidine-2-thione
SMILES:[H][C@@]1(CO)O[C@]([H])(N2C=C(CNC)C(O)=NC2=S)[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
  • 2-thiopyrimidine
  • Thiopyrimidine
  • Aralkylamine
  • Pyrimidone
  • Pyrimidinethione
  • Pyrimidine
  • Monosaccharide
  • Hydropyrimidine
  • Heteroaromatic compound
  • Vinylogous amide
  • Tetrahydrofuran
  • Thiourea
  • Secondary alcohol
  • Lactam
  • Oxacycle
  • Azacycle
  • Organoheterocyclic compound
  • Secondary amine
  • Secondary aliphatic amine
  • Organic nitrogen compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organosulfur 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 Solubility2.6 g/LALOGPS
logP-1.4ALOGPS
logP-3.3ChemAxon
logS-2.1ALOGPS
pKa (Strongest Acidic)7.74ChemAxon
pKa (Strongest Basic)9.22ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area117.78 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity73.44 m³·mol⁻¹ChemAxon
Polarizability29.61 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_3_4) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-00di-0921000000-7dd67f46acaf758a4821View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00dl-1900000000-95cde416935abdfdce8dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-022c-5900000000-fe55b83c3ea1b2882b74View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0udi-3469000000-97caf3bb7e171c289664View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-00ec-2910000000-9ffb3a6eec7ebbede784View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4i-9500000000-1b3a2eb33e858d83ceedView 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
  • Stadtman, T. C. (1983). "New biologic functions--selenium-dependent nucleic acids and proteins." Fundam Appl Toxicol 3:420-423. Pubmed: 6227514
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • 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 ID3036488
Kegg IDNot Available
ChemSpider ID2300488
Wikipedia IDNot Available
BioCyc ID5-METHYLAMINOMETHYL-2-THIOURIDINE
EcoCyc ID5-METHYLAMINOMETHYL-2-THIOURIDINE

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.