Modomics - A Database of RNA Modifications

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


Full name5-carboxymethylaminomethyl-2-selenouridine
Short namecmnm5se2U
MODOMICS code new2000002051U
MODOMICS code2051U
Nature of the modified residueNatural
RNAMods code
Residue unique ID54
Found in RNAYes
Related nucleotides394
Enzymes MnmH (Escherichia coli)
MnmE (Escherichia coli)
MnmE (Chlorobium tepidum)
MnmE (Nostoc sp.)
MnmE (Thermotoga maritima)
MnmG (Escherichia coli)
MnmG (Chlorobium tepidum)
MnmG (Aquifex aeolicus)
Found in phylogenyEubacteria

Chemical information

Sum formulaC12H17N3O7Se
Type of moietynucleoside
Degeneracynot applicable
Number of atoms23
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand 38T
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
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 SMILES
O=C(CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])[nH]c1=O)O tautomer #0
OC(C=NCc1cn(C2OC(CO)C(O)C2O)c(=[Se])[nH]c1=O)O tautomer #1
OC(=CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])[nH]c1=O)O tautomer #2
O=C(CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])nc1O)O tautomer #3
OC(C=NCc1cn(C2OC(CO)C(O)C2O)c(=[Se])nc1O)O tautomer #4
OC(=CNCc1cn(C2OC(CO)C(O)C2O)c(=[Se])nc1O)O tautomer #5
Tautomer image Show Image

Predicted CYP Metabolic Sites

cmnm5se2U cmnm5se2U cmnm5se2U

* 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 mass393.0239
Average mass394.239
Product ions262
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

aminoacyl groupglycyl
heavy atomselenium
methyl groupmethyl at aromatic C
othersecondary amine

Reactions producing 5-carboxymethylaminomethyl-2-selenouridine


Reactions starting from 5-carboxymethylaminomethyl-2-selenouridine


Last modification of this entry: Sept. 22, 2023