Modomics - A Database of RNA Modifications

pm5U
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
See the molecule on the similarity map

Summary

Full name5-methyluridine-5'-monophosphate
IUPAC name[(2R,3S,4R,5R)-3,4-dihydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl phosphate
Short namepm5U
MODOMICS code new2000005551U
MODOMICS code5551U
Synonyms
5-methyl-5'-O-phosphonatouridine
5-methyl-UMP
CHEBI:142797
m(5)UMP
TMP(2-)
Nature of the modified residueNatural
RNAMods codeT
Residue unique ID194
Found in RNAYes
Related nucleosides12
RCSB ligands

5MU


Chemical information

Sum formulaC10H12N2O9P
Type of moietynucleotide
Degeneracynot aplicable
SMILES[C@H]1([n]2cc(C)c(=O)nc2=O)[C@H](O)[C@H](O)[C@@H](COP([O-])([O-])=O)O1
logP-1.0731
TPSA169.3
Number of atoms22
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)2
InChIInChI=1S/C10H14N2O9P/c1-4-2-12(10(16)11-8(4)15)9-7(14)6(13)5(21-9)3-20-22(17,18)19/h2,5-7,9,13-14H,3H2,1H3,(H2,17,18,19)/p-2/t5-,6-,7-,9-/m1/s1
InChIKeySWDFLKFMJOONJB-JXOAFFINSA-L
Search the molecule in external databases ChEMBL  PubChem Compound Database  Ligand Expo  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)

QM Data:

Dipole Magnitude [D]:30.078524145
Energy [Eh]:-1516.62399034791
HOMO [eV]:-8.5015
LUMO [eV]:0.9768
Gap [eV]:9.4783

Download QM Data:

Charges   charge.txt

Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb


LC-MS Information

Monoisotopic massNone
Average mass335.184
[M+H]+ not available
Product ions not available
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.

Last modification of this entry: Sept. 15, 2025