Summary

Full name5-methoxycarbonylmethyl-2-thiouridine
IUPAC namemethyl 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]acetate
Short namemcm5s2U
MODOMICS code2521U
Synonyms
20299-15-4
5-(2-methoxy-2-oxoethyl)-1-(beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one
5-(2-methoxy-2-oxoethyl)2-thiouridin
5-methoxycarbonylmethyl-2-thiouridine
CHEBI:20597
J-013194
mcm(5)s(2)u
mcm5s2U
methyl 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]acetate
Q27109315
SCHEMBL64611

Nature of the modified residueNatural
RNAMods code3
Residue unique ID68
Found in RNAYes
Related nucleotides223
Enzymes ALKBH8 (Homo sapiens)
Ncs6 (Saccharomyces cerevisiae)
Trm9 (Saccharomyces cerevisiae)
Ncs2 (Saccharomyces cerevisiae)
TrmU (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H16N2O7S
Type of moietynucleoside
Degeneracynot applicable
SMILESCOC(Cc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O)=O
logP-1.7671
TPSA166.1
Number of atoms22
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 70U
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0011610
InChIInChI=1S/C12H16N2O7S/c1-20-7(16)2-5-3-14(12(22)13-10(5)19)11-9(18)8(17)6(4-15)21-11/h3,6,8-9,11,15,17-18H,2,4H2,1H3,(H,13,19,22)/t6-,8-,9-,11-/m1/s1
InChIKeyHLZXTFWTDIBXDF-PNHWDRBUSA-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
COC(C=C1CN(C2OC(CO)C(O)C2O)C(=S)NC1=O)=O tautomer #0
COC(Cc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)=O tautomer #1
COC(C=C1CN(C2OC(CO)C(O)C2O)C(S)=NC1=O)=O tautomer #2
COC(Cc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)=O tautomer #3
COC(=Cc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #4
COC(=Cc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #5
COC(C=C1CN(C2OC(CO)C(O)C2O)C(=S)N=C1O)=O tautomer #6
COC(Cc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)=O tautomer #7
COC(=Cc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #8

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mcm5s2U mcm5s2U mcm5s2U

* 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 mass332.0678
Average mass332.33
[M+H]+333.0756
Product ions201/169/141
Normalized LC elution time *1,78 (Kellner 2014)
LC elution order/characteristicsbetween A and m6A (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 -
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -

Chemical groups contained

TypeSubtype
heavy atomsulfur
othercarboxymethyl
othermethylester

Reactions producing 5-methoxycarbonylmethyl-2-thiouridine

Name
cm5s2U:mcm5s2U
mcm5U:mcm5s2U

Last modification of this entry: Sept. 29, 2021


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