Full name5-cyanomethyluridine
Short namecnm5U
Nature of the modified residueNatural
RNAMods codeѶ
Residue unique ID178
Found in RNAYes
Related nucleotides396

Chemical information

Sum formulaC11H13N3O6
Type of moietynucleoside
Degeneracynot applicable
Number of atoms20
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)4
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
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* 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
N#CCc1cn(C2OC(CO)C(O)C2O)c(=O)[nH]c1=O tautomer #0
N#CCc1cn(C2OC(CO)C(O)C2O)c(O)nc1=O tautomer #1
N#CCc1cn(C2OC(CO)C(O)C2O)c(=O)nc1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

cnm5U cnm5U cnm5U

* 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 mass283.0804
Average mass283.237
Product ions152
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.


Identified in mutant tRNAIle from Haloarcula marismortui. Present in total tRNAs from euryarchaea but not in crenarchaea, eubacteria, or eukaryotes.

Chemical groups contained

methyl groupmethyl at aromatic C

Last modification of this entry: Sept. 29, 2021

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