Summary

Full name2-thiouridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-sulfanylidenepyrimidin-4-one
Short names2U
MODOMICS code2U
Synonyms
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-sulfanylidenepyrimidin-4-one
1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-2-thioxo-pyrimidin-4-one
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-4-hydroxy-pyrimidine-2-thione
1-((2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one?s2U; AC1MI168, CHEBI:60731
1-beta-D-ribofuranosyl-2-thiouracil
1-beta-D-ribofuranosyl-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
1-(beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
20235-78-3
235T783
2-Thio-D-uridine
2-thiouridine
2TU
3sfg
7-ETHOXYCARBONYLAMINO-1-OXO-1,2,3,4-TETRAHYDRO-ISOQUINOLINE
A3104/0131463
AC1MI168
AKOS025149643
AM84694
AS-10679
beta-D-ribofuranosyl-2-thiouridine
C9-H12-N2-O5-S
CHEBI:60731
CID3036443
CTK1A7238
DTXSID90174087
GJTBSTBJLVYKAU-XVFCMESISA-N
MFCD03788697
N/A
Q20890502
s2U
SC-14804
SCHEMBL41558
THIOURIDINE
Uridine, 2-thio-
ZINC4501448

Nature of the modified residueNatural
RNAMods code2
Residue unique ID100
Found in RNAYes
Related nucleotides187
Enzymes MnmA (Escherichia coli)
Mtu1 (Saccharomyces cerevisiae)
Ncs2 (Saccharomyces cerevisiae)
Ncs6 (Saccharomyces cerevisiae)
TrmU (Homo sapiens)
Found in phylogenyEubacteria, Eukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC9H12N2O5S
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3036443
SMILESO[C@H]1[C@H]([n]2ccc(=O)[nH]c2=S)O[C@H](CO)[C@H]1O
logP-1.4826
TPSA139.8
Number of atoms17
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 2TU
PDB exact match , link to the most similar ligand 2TU
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C9H12N2O5S/c12-3-4-6(14)7(15)8(16-4)11-2-1-5(13)10-9(11)17/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,17)/t4-,6-,7-,8-/m1/s1
InChIKeyGJTBSTBJLVYKAU-XVFCMESISA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)


Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb

Tautomers

Tautomers SMILES
OC1C(n2ccc(=O)[nH]c2=S)OC(CO)C1O tautomer #0
OC1C(n2ccc(=O)nc2S)OC(CO)C1O tautomer #1
OC1C(n2ccc(O)nc2=S)OC(CO)C1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
s2U s2U s2U

* CYP Metabolic sites predicted with SMARTCyp. SMARTCyp is a method for prediction of which sites in a molecule that are most liable to metabolism by Cytochrome P450. It has been shown to be applicable to metabolism by the isoforms 1A2, 2A6, 2B6, 2C8, 2C19, 2E1, and 3A4 (CYP3A4), and specific models for the isoform 2C9 (CYP2C9) and isoform 2D6 (CYP2D6). CYP3A4, CYP2D6, and CYP2C9 are the three of the most important enzymes in drug metabolism since they are involved in the metabolism of more than half of the drugs used today. The three top-ranked atoms are highlighted. See: SmartCYP and SmartCYP - background; Patrik Rydberg, David E. Gloriam, Lars Olsen, The SMARTCyp cytochrome P450 metabolism prediction server, Bioinformatics, Volume 26, Issue 23, 1 December 2010, Pages 2988–2989 (link)


LC-MS Information

Monoisotopic mass260.0467
Average mass260.267
[M+H]+261.0545
Product ions129
Normalized LC elution time *1,06 (Kellner 2014)
LC elution order/characteristicsbetween G and A (Kellner 2014)

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Absolute and relative quantification of RNA modifications via biosynthetic isotopomers. Kellner S, Ochel A, Thuring K, Spenkuch F, Neumann J, Sharma S, Entian KD, Schneider D, Helm M... Nucleic Acids Res [details] 25129236 -

Chemical groups contained

TypeSubtype
heavy atomsulfur

Reactions producing 2-thiouridine

Name
U:s2U

Reactions starting from 2-thiouridine

Name
s2U:se2U
s2U:nm5s2U
s2U:cmnm5s2U
s2U:tm5s2U
s2U:s2Um
s2U:ges2U

Last modification of this entry: Sept. 29, 2021


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