Modomics - A Database of RNA Modifications

mo5U
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

Summary

Full name5-methoxyuridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methoxypyrimidine-2,4-dione
Short namemo5U
MODOMICS code new2000000501U
MODOMICS code501U
Synonyms
1-[(2R,3R,4R,5R)-3,4-Dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methoxypyrimidine-2,4-dione
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methoxypyrimidine-2,4-dione
1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methoxypyrimidine-2,4(1H,3H)-dione
35542-01-9
5-Methoxyuridine
AC1LOMX5
AC-32337
AKOS025146635
C10-H14-N2-O7
C10H14N2O7
CHEBI:20601
CID1265899
CTK1C5565
EINECS 252-609-8
MFCD00006533
mo(5)u
NS00059240
SCHEMBL41141
Uridine, 5-methoxy-
Uridine,5-methoxy-
ZB015843
ZINC1078619
Nature of the modified residueNatural
RNAMods code5
Residue unique ID74
Found in RNAYes
Related nucleotides363
Enzymes CmoB (Escherichia coli)
TrmR (Bacillus subtilis)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC10H14N2O7
Type of moietynucleoside
Degeneracynot applicable
PubChem ID169704
SMILESCOc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1
logP-2.8433
TPSA134.01
Number of atoms19
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 URI
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C10H14N2O7/c1-18-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)19-9/h2,5-7,9,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,9-/m1/s1
InChIKeyZXIATBNUWJBBGT-JXOAFFINSA-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
COc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #0
COc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #1
COc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1 tautomer #2
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mo5U mo5U mo5U

* 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 mass274.0801
Average mass274.227
[M+H]+275.0879
Product ions143
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.

Comments

mo5U is a modification characteristic for gram positive bacteria (B. subtilis, Firmicutes). Gram negative bacteria have cmo5U and mcmo5U in this position (E. coli, Protebacteria). Null mutation of cmoA in S. enterica results in the accummulation of tRNA containing mo5U34 and ho5U34.

Chemical groups contained

TypeSubtype
othermethoxy

Reactions producing 5-methoxyuridine

Name
ho5U:mo5U
ho5U:mo5U

Reactions starting from 5-methoxyuridine

Name
mo5U:cmo5U

Publications

Title Authors Journal Details PubMed Id DOI
The modified wobble nucleoside uridine-5-oxyacetic acid in tRNAPro(cmo5UGG) promotes reading of all four proline codons in vivo. Nasvall SJ, Chen P, Bjork GR RNA [details] 15383682 -
5-methoxyuridine: a new minor constituent located in the first position of the anticodon of tRNAAla, tRNAThr, and tRNAVal from Bacillus subtilis. Murao K, Hasegawa T, Ishikura H Nucleic Acids Res [details] 825836 -

Last modification of this entry: Sept. 22, 2023