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-(isopentenylaminomethyl)uridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-[(3-methylbut-2-enylamino)methyl]pyrimidine-2,4-dione
Short nameinm5U
MODOMICS code new2000000583U
Nature of the modified residueNatural
RNAMods code¾
Residue unique ID144
Found in RNAYes
Related nucleotides354

Chemical information

Sum formulaC15H23N3O6
Type of moietynucleoside
Degeneracynot applicable
Number of atoms24
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)5
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
CC(=CCNCc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)C tautomer #0
CC(=CCNCc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)C tautomer #1
CC(=CCNCc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)C tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

inm5U inm5U inm5U

* 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 mass341.1587
Average mass341.36
Product ions210
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.


5-(isopentenylaminomethyl)uridine and 2-thio-5-(isopentenylaminomethyl)uridine were identified in tRNA of Thermodesulfobacterium commune. Their identities were determined by mass spectrometry and confirmed by chemical synthesis. Data were presented at the tRNA meeting in Banz, Germany (1985) by P.F. Crain, D.R. Phillips, T. Hashizume and F. Widdel. Since then, beside the Banz-meeting abstract, no paper was published about these modified nucleosides.

Reactions producing 5-(isopentenylaminomethyl)uridine


Reactions starting from 5-(isopentenylaminomethyl)uridine


Last modification of this entry: Sept. 22, 2023