Summary

Full name5-carboxymethylaminomethyl-2-thiouridine
IUPAC name2-[[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]methylamino]acetic acid
Short namecmnm5s2U
MODOMICS code251U
Synonyms
2-[[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-oxo-2-sulfanylidenepyrimidin-5-yl]methylamino]acetic acid
2-(((1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl)amino)acetic acid
2-thio-5-{[(carboxymethyl)amino]methyl}uridine
5-Carboxymethylaminomethyl-2-thiouridine
5-(Carboxymethylaminomethyl)-2-thiouridine
5-Cmtu
78173-95-2
AC1MI3NX
CHEBI:64336
CID3037867
cmnm(5)s(2)u
CTK5E5473
DTXSID60228824
Glycine, N-((1,2,3,4-tetrahydro-4-oxo-1-beta-D-ribofuranosyl-2-thioxo-5-pyrimidinyl)methyl)-
Glycine,N-[(1,2,3,4-tetrahydro-4-oxo-1-b-D-ribofuranosyl-2-thioxo-5-pyrimidinyl)methyl]-
N-{[4-oxo-1-(beta-D-ribofuranosyl)-2-thioxo-1,2,3,4-tetrahydropyrimidin-5-yl]methyl}glycine
Q27133223
SCHEMBL104678

Nature of the modified residueNatural
RNAMods code$
Residue unique ID45
Found in RNAYes
Related nucleotides395
Enzymes MnmA (Escherichia coli)
Mtu1 (Saccharomyces cerevisiae)
TrmU (Homo sapiens)
MnmE (Escherichia coli)
MnmE (Chlorobium tepidum)
MnmE (Nostoc sp.)
MnmE (Thermotoga maritima)
MnmG (Escherichia coli)
MnmG (Chlorobium tepidum)
MnmG (Aquifex aeolicus)
Mss1 (Saccharomyces cerevisiae)
Mto1 (Saccharomyces cerevisiae)
Found in phylogenyEubacteria, Eukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H17N3O7S
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3037867
SMILESOC(CNCc1c[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=S)[nH]c1=O)=O
logP-1.9175
TPSA189.13
Number of atoms23
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand U8U
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0011610
InChIInChI=1S/C12H17N3O7S/c16-4-6-8(19)9(20)11(22-6)15-3-5(1-13-2-7(17)18)10(21)14-12(15)23/h3,6,8-9,11,13,16,19-20H,1-2,4H2,(H,17,18)(H,14,21,23)/t6-,8-,9-,11-/m1/s1
InChIKeyVKLFQTYNHLDMDP-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
O=C(CNCc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #0
OC(C=NCc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #1
O=C(CNCc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #2
OC(C=NCc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #3
OC(=CNCc1cn(C2OC(CO)C(O)C2O)c(=S)[nH]c1=O)O tautomer #4
O=C(CNCc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #5
OC(C=NCc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #6
OC(=CNCc1cn(C2OC(CO)C(O)C2O)c(S)nc1=O)O tautomer #7
OC(=CNCc1cn(C2OC(CO)C(O)C2O)c(=S)nc1O)O tautomer #8

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
cmnm5s2U cmnm5s2U cmnm5s2U

* 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 mass347.0787
Average mass347.344
[M+H]+348.0865
Product ions255/273/141/216/237/225
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.

Chemical groups contained

TypeSubtype
aminoacyl groupglycyl
heavy atomsulfur
methyl groupmethyl at aromatic C
othersecondary amine

Reactions producing 5-carboxymethylaminomethyl-2-thiouridine

Name
cmnm5U:cmnm5s2U
s2U:cmnm5s2U

Reactions starting from 5-carboxymethylaminomethyl-2-thiouridine

Name
cmnm5s2U:nm5s2U
cmnm5s2U:cmnm5se2U
cmnm5s2U:cmnm5ges2U

Last modification of this entry: Sept. 29, 2021


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