Modomics - A Database of RNA Modifications

s2C
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

Summary

Full name2-thiocytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2-thione
Short names2C
MODOMICS code new2000000002C
MODOMICS code2C
Synonyms
13239-97-9
2(1H)-Pyrimidinethione, 4-amino-1-.beta.-D-ribofuranosyl-
2-Thiocytidine
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2-thione
4-Amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidine-2(1H)-thione
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidine-2-thione
4-amino-1-beta-D-ribofuranosylpyrimidine-2(1H)-thione
AC1MHUQ1
beta-D-ribofuranosyl-2-thiocytidine
BRD-K67390410-001-01-2
C9-H13-N3-O4-S
C9H13N3O4S
CHEBI:19780
CID3011746
CTK0H9573
Cytidine, 2-thio-
DTXSID30157516
EINECS 236-214-8
N/A
NS00024211
Q20890505
SCHEMBL42103
ZINC13516196
Nature of the modified residueNatural
RNAMods code%
Residue unique ID92
Found in RNAYes
Related nucleotides347
Enzymes TtcA (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC9H13N3O4S
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3011746
SMILESNc1nc(=S)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)cc1
logP-0.6125
TPSA145.85
Number of atoms17
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand RSP
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C9H13N3O4S/c10-5-1-2-12(9(17)11-5)8-7(15)6(14)4(3-13)16-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,17)/t4-,6-,7-,8-/m1/s1
InChIKeyRHFUOMFWUGWKKO-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
N=c1[nH]c(=S)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #0
N=c1nc(S)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #1
Nc1nc(=S)n(C2C(O)C(O)C(CO)O2)cc1 tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
s2C s2C s2C

* 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 mass259.0627
Average mass259.282
[M+H]+260.0705
Product ions128
Normalized LC elution time *0,68 (Kellner 2014); 0,86 (Kellner 2014)
LC elution order/characteristicsbetween U and G (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 -

Comments

s2C at position 32 in bacterial tRNA allows more anticodon loop flexibility that limit formation of the characteristic U33-turn conformation of anticodon loop in other tRNA lacking s2C32.

Chemical groups contained

TypeSubtype
heavy atomsulfur

Reactions producing 2-thiocytidine

Name
C:s2C

Publications

Title Authors Journal Details PubMed Id DOI
Modifications Modulate Anticodon Loop Dynamics and Codon Recognition of E. coli tRNA(Arg1,2). Cantara WA, Bilbille Y, Kim J, Kaiser R, Leszczyńska G, Malkiewicz A, Agris PF J Mol Biol [details] 22240457 -
Thiobases in Escherchia coli Transfer RNA: 2-Thiocytosine and 5-Methylaminomethyl-2-thiouracil. Carbon J, David H, Studier MH Science [details] 17812290 -

Last modification of this entry: Sept. 22, 2023