Summary
| Full name | 4-thiouridine |
| IUPAC name | 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylidenepyrimidin-2-one |
| Short name | s4U |
| MODOMICS code new | 2000000074U |
| MODOMICS code | 74U |
| Synonyms |
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylidene-1,2,3,4-tetrahydropyrimidin-2-one
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-sulfanylidenepyrimidin-2-one 1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-4-thioxo-3,4-dihydropyrimidin-2(1H)-one 1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-4-thioxo-pyrimidin-2-one 13957-31-8 1-beta-D-ribofuranosyl-4-thiouracil 1-(beta-D-ribofuranosyl)-4-thioxo-3,4-dihydropyrimidin-2(1H)-one 4 Thiouridine 4-Thio-D-uridine 4-thioribothymidine 4-thio-uridine 4-Thiouridine 4-Thiouridine, >=98% 4-Thiouridine, 98% - 10MG 10mg AC1MHUF8 AS-56720 C9-H12-N2-O5-S CHEBI:20480 CID3032615 CS-W012509 CTK4C1864 D013891 EINECS 237-735-3 EX-A3667 KS-00000Y8U LS-187054 LS-187666 MFCD00006538 N/A NSC 518132 Q20890501 s4T S4U SCHEMBL34577 THIOURIDINE Thiouridine (VAN) Uridine, 4-thio- Uridine, 4-thio- (8CI)(9CI) Uridine,4-thio- ZINC13518039 ZLOIGESWDJYCTF-XVFCMESISA-N |
| Nature of the modified residue | Natural |
| RNAMods code | 4 |
| Residue unique ID | 7 |
| Found in RNA | Yes |
| Related nucleotides | 216 |
| Enzymes |
ThiI (Escherichia coli) |
| Found in phylogeny | Eubacteria |
| Found naturally in RNA types | tRNA |
Chemical information
| Sum formula | C9H12N2O5S |
| Type of moiety | nucleoside |
| Degeneracy | not applicable |
| PubChem ID | 3954028 |
| SMILES | OC[C@H]1O[C@@H]([n]2ccc(=S)[nH]c2=O)[C@H](O)[C@@H]1O |
| logP | -1.4826 |
| TPSA | 139.8 |
| Number of atoms | 17 |
| 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 | ZE8 |
| HMDB (Human Metabolome Database) no exact match, link to the most similar ligand | None |
| InChI | InChI=1S/C9H12N2O5S/c12-3-4-6(13)7(14)8(16-4)11-2-1-5(17)10-9(11)15/h1-2,4,6-8,12-14H,3H2,(H,10,15,17)/t4-,6-,7-,8-/m1/s1 |
| InChIKey | ZLOIGESWDJYCTF-XVFCMESISA-N |
| Search the molecule in external databases | ChEMBL ChemAgora ChEBI PubChem Compound Database Ligand Expo ChemSpider WIPO |
| PubChem CID | |
| PubChem SIDs |
10047324
14750149 14848014 16121002 24900212 36076798 50070591 50071202 50518728 57352696 88877558 104222119 111632563 129920222 134990572 140033847 143178760 161004319 162227313 162790182 225059302 226421020 250133687 252225459 252341193 252400682 252415454 254766299 259323607 274892841 310104581 310280936 312237538 316538853 316580836 319257237 319441327 341238273 342526821 342597057 346441140 347244819 347734933 347759002 348741411 354319222 355126382 363671169 374046590 375198022 375286458 376073976 376243003 377539349 381013302 381028185 385647740 386258777 386484146 387023243 388664057 404824238 405045926 419579761 433909746 434138339 434400795 438445224 439508027 442119795 443501262 |
* 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 |
OCC1OC(n2ccc(S)nc2=O)C(O)C1O tautomer #0
OCC1OC(n2ccc(=S)[nH]c2=O)C(O)C1O tautomer #1 OCC1OC(n2ccc(=S)nc2O)C(O)C1O tautomer #2 |
| Tautomer image | Show Image |
Predicted CYP Metabolic Sites
| CYP3A4 | CYP2D6 | CYP2C9 |
|---|---|---|
|
|
|
* 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 mass | 260.0467 |
| Average mass | 260.267 |
| [M+H]+ | 261.0545 |
| Product ions | 129 |
| Normalized LC elution time * | 1,15 (Kellner 2014); 1,18 (Kellner 2014) |
| LC elution order/characteristics | between G and A (Kellner 2014, 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 | ||
|---|---|---|---|---|---|
| Profiling of RNA modifications by multiplexed stable isotope labelling. | Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. | Chem Commun (Camb). | [details] | 24567952 | - |
| 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
| Type | Subtype |
|---|---|
| heavy atom | sulfur |
Reactions producing 4-thiouridine
| Name |
|---|
| U:s4U |
Last modification of this entry: Sept. 22, 2023