Summary

Full name5-carboxymethylaminomethyluridine
IUPAC name2-[[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]methylamino]acetic acid
Short namecmnm5U
MODOMICS code51U
Synonyms
2-[[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]methylamino]acetic acid
2-(((1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)methyl)amino)acetic acid
5-(( uridine
5-carboxymethylaminomethyluridine
5-(((Carboxymethyl)amino)methyl)uridine
5-(Carboxymethylaminomethyl)uridine
69181-26-6
8063-24-9
AC1L4XZM
AC1Q5WOW
Acriflavine hydrochloride
AR-1L8083
CHEBI:64337
CID194306
CMAMU
cmnm(5)u
CTK5C9194
DTXSID50988889
Glycine, N-((1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-5-pyrimidinyl)methyl)-
Glycine,N-[(1,2,3,4-tetrahydro-2,4-dioxo-1-b-D-ribofuranosyl-5-pyrimidinyl)methyl]-
N-{[2,4-dioxo-1-(beta-D-ribofuranosyl)-1,2,3,4-tetrahydropyrimidin-5-yl]methyl}glycine
N-[(4-Hydroxy-2-oxo-1-pentofuranosyl-1,2-dihydropyrimidin-5-yl)methyl]glycine
Q27133224
SCHEMBL41270
uridine, 5-[[(carboxymethyl)amino]methyl]-

Nature of the modified residueNatural
RNAMods code!
Residue unique ID87
Found in RNAYes
Related nucleotides358
Enzymes 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 formulaC12H17N3O8
Type of moietynucleoside
Degeneracynot applicable
PubChem ID194306
SMILESOC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(CNCC(=O)O)c2)O1
logP-3.2868
TPSA174.11
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 38T
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000884
InChIInChI=1S/C12H17N3O8/c16-4-6-8(19)9(20)11(23-6)15-3-5(1-13-2-7(17)18)10(21)14-12(15)22/h3,6,8-9,11,13,16,19-20H,1-2,4H2,(H,17,18)(H,14,21,22)/t6-,8-,9-,11-/m1/s1
InChIKeyVSCNRXVDHRNJOA-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
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(CNCC(O)=O)c2)O1 tautomer #0
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(CN=CC(O)O)c2)O1 tautomer #1
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(CNC=C(O)O)c2)O1 tautomer #2
OCC1C(O)C(O)C(n2c(O)nc(=O)c(CNCC(O)=O)c2)O1 tautomer #3
OCC1C(O)C(O)C(n2c(O)nc(=O)c(CN=CC(O)O)c2)O1 tautomer #4
OCC1C(O)C(O)C(n2c(=O)nc(O)c(CNCC(O)=O)c2)O1 tautomer #5
OCC1C(O)C(O)C(n2c(=O)nc(O)c(CN=CC(O)O)c2)O1 tautomer #6
OCC1C(O)C(O)C(n2c(O)nc(=O)c(CNC=C(O)O)c2)O1 tautomer #7
OCC1C(O)C(O)C(n2c(=O)nc(O)c(CNC=C(O)O)c2)O1 tautomer #8

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
cmnm5U cmnm5U cmnm5U

* 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 mass331.1016
Average mass331.279
[M+H]+332.1094
Product ions239/257/209/125/200/221
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
methyl groupmethyl at aromatic C
othersecondary amine

Reactions producing 5-carboxymethylaminomethyluridine

Name
U:cmnm5U

Reactions starting from 5-carboxymethylaminomethyluridine

Name
cmnm5U:nm5U
cmnm5U:cmnm5Um
cmnm5U:cmnm5s2U

Last modification of this entry: Sept. 29, 2021


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