Modomics - A Database of RNA Modifications

The molecule is shown in a ball-and-stick representation with the following colors for atoms :

⬤ Hydrogen (H): white ⬤ Carbon (C): gray ⬤ Oxygen (O): red ⬤ Phosphorus (P): orange ⬤ Nitrogen (N): blue ⬤ Selenium (Se): gold ⬤ Sulfur (S): yellow

See the molecule on the similarity map

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
ChEBI ID	20480
CAS Registry Number	13957-31-8
Reaxys Registry Number	28750
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
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 PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	3032615
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)

QM Data:

Dipole Magnitude [D]:	12.030928206
Energy [Eh]:	-1233.59660367575
HOMO [eV]:	-8.9449
LUMO [eV]:	-0.1689
Gap [eV]:	8.776

Download QM Data:

Cube	.cube
Charges	charge.txt

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	PubMed Id	DOI
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. 15, 2025