Summary

Full name5-carboxymethyl-2-thiouridine
IUPAC name2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]acetic acid
Short namecm5s2U
MODOMICS code2540U
Synonyms
2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]acetic acid
2-Thio-5-carboxymethyluridine
58479-77-9
5-carboxymethyl-2-thiouridine
5-Pyrimidineacetic acid, 1,2,3,4-tetrahydro-4-oxo-1-beta-D-ribofuranosyl-2-thioxo-
5-Pyrimidineacetic acid, 1,2,3,4-tetrahydro-4-oxo-1-.beta.-D-ribofuranosyl-2-thioxo-
AC1MI3AE
CID3037666
DTXSID80207171
SCHEMBL9198399

Nature of the modified residueNatural
RNAMods code
Residue unique ID11
Found in RNAYes
Related nucleotides391
Found in phylogenyEukaryota

Chemical information

Sum formulaC11H14N2O7S
Type of moietynucleoside
Degeneracynot applicable
SMILESOC(Cc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O)=O
logP-1.8555
TPSA177.1
Number of atoms21
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)5
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/C11H14N2O7S/c14-3-5-7(17)8(18)10(20-5)13-2-4(1-6(15)16)9(19)12-11(13)21/h2,5,7-8,10,14,17-18H,1,3H2,(H,15,16)(H,12,19,21)/t5-,7-,8-,10-/m1/s1
InChIKeyMSGFOEBMIJOVCL-VPCXQMTMSA-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
O=C(Cc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #0
O=C(C=C1CN(C2OC(CO)C(O)C2O)C(=S)NC1=O)O tautomer #1
O=C(Cc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #2
O=C(C=C1CN(C2OC(CO)C(O)C2O)C(S)=NC1=O)O tautomer #3
OC(=Cc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #4
O=C(Cc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #5
O=C(C=C1CN(C2OC(CO)C(O)C2O)C(=S)N=C1O)O tautomer #6
OC(=Cc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #7
OC(=Cc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #8

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
cm5s2U cm5s2U cm5s2U

* 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 mass318.0522
Average mass318.303
[M+H]+319.06
Product ions187/169/141
Normalized LC elution time * not available
LC elution order/characteristics not available

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Comments

This is an artificial substrate obtained by alkaline hydrolysis of mcm5s2U.

Chemical groups contained

TypeSubtype
heavy atomsulfur
othercarboxymethyl

Reactions starting from 5-carboxymethyl-2-thiouridine

Name
cm5s2U:mcm5s2U

Last modification of this entry: Sept. 29, 2021


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