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	2-thiouridine
IUPAC name	1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2-sulfanylidenepyrimidin-4-one
Short name	s2U
MODOMICS code new	2000000002U
MODOMICS code	2U
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 residue	Natural
RNAMods code	2
Residue unique ID	100
Found in RNA	Yes
Related nucleotides	187
Enzymes	MnmA (Escherichia coli) Mtu1 (Saccharomyces cerevisiae) Ncs2 (Saccharomyces cerevisiae) Ncs6 (Saccharomyces cerevisiae) TrmU (Homo sapiens)
Found in phylogeny	Eubacteria, Eukaryota
Found naturally in RNA types	tRNA

Chemical information

Sum formula	C9H12N2O5S
Type of moiety	nucleoside
Degeneracy	not applicable
PubChem ID	3036443
ChEBI ID	60731
Reaxys Registry Number	28752
SMILES	O[C@H]1[C@H]([n]2ccc(=O)[nH]c2=S)O[C@H](CO)[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(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
InChIKey	GJTBSTBJLVYKAU-XVFCMESISA-N
Search the molecule in external databases	ChEMBL ChemAgora PubChem Compound Database Ligand Expo ChemSpider WIPO
PubChem CID	3036443
PubChem SIDs	1968 10048541 16583677 36104609 75309259 103158591 111641311 127963888 135102924 135668444 162501609 163662279 170484093 171579113 175438200 224148828 226426562 241059388 252228207 252400681 252417392 252672150 257295623 273550410 310280935 312241741 315734493 318166307 318488398 319259294 319461592 321933247 329883566 341154407 341836822 342526819 342597592 346566825 347752890 348885581 354265282 354308645 355046387 355099664 363671151 374092592 375124562 375553715 375973625 376018442 376472372 377598243 378020180 381028162 381319605 382422630 385647741 386484147 403601572 404825190 419563518 434737977 436396357 438539093 439476969 440080483 443501263 443554408

^* 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]:	4.351512856
Energy [Eh]:	-1233.59047955206
HOMO [eV]:	-9.2
LUMO [eV]:	0.3692
Gap [eV]:	9.5692

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	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

^* 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^*	1,06 (Kellner 2014)
LC elution order/characteristics	between 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

Type	Subtype
heavy atom	sulfur

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. 15, 2025