Summary
| Full name | uridine 5-oxyacetic acid methyl ester |
| Short name | mcmo5U |
| MODOMICS code new | 2000000503U |
| MODOMICS code | 503U |
| Nature of the modified residue | Natural |
| RNAMods code | υ |
| Residue unique ID | 58 |
| Found in RNA | Yes |
| Related nucleotides | 425 |
| Found in phylogeny | Eubacteria |
| Found naturally in RNA types | tRNA |
Chemical information
| Sum formula | C12H16N2O9 |
| Type of moiety | nucleoside |
| Degeneracy | not applicable |
| PubChem ID | 191808 |
| SMILES | COC(COc1c[n](C2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)[nH]c1=O)=O |
| logP | -3.3001 |
| TPSA | 160.31 |
| Number of atoms | 23 |
| Number of Hydrogen Bond Acceptors 1 (HBA1) | 9 |
| Number of Hydrogen Bond Acceptors 2 (HBA2) | 10 |
| Number of Hydrogen Bond Donors (HBD) | 4 |
| PDB no exac match , link to the most similar ligand | CM0 |
| HMDB (Human Metabolome Database) no exact match, link to the most similar ligand | None |
| InChI | InChI=1S/C12H16N2O9/c1-21-7(16)4-22-5-2-14(12(20)13-10(5)19)11-9(18)8(17)6(3-15)23-11/h2,6,8-9,11,15,17-18H,3-4H2,1H3,(H,13,19,20)/t6-,8-,9-,11?/m1/s1 |
| InChIKey | WZRYXYRWFAPPBJ-ABHRNEANSA-N |
| 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
| Tautomers SMILES |
COC(COc1cn(C2OC(CO)C(O)C2O)c(=O)[nH]c1=O)=O tautomer #0
COC(=COc1cn(C2OC(CO)C(O)C2O)c(=O)[nH]c1=O)O tautomer #1 COC(COc1cn(C2OC(CO)C(O)C2O)c(O)nc1=O)=O tautomer #2 COC(COc1cn(C2OC(CO)C(O)C2O)c(=O)nc1O)=O tautomer #3 COC(=COc1cn(C2OC(CO)C(O)C2O)c(O)nc1=O)O tautomer #4 COC(=COc1cn(C2OC(CO)C(O)C2O)c(=O)nc1O)O tautomer #5 |
| Tautomer image | Show Image |
Predicted CYP Metabolic Sites
| CYP3A4 | CYP2D6 | CYP2C9 |
|---|---|---|
|
|
|
* 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 mass | 332.0856 |
| Average mass | 332.263 |
| [M+H]+ | 333.0934 |
| Product ions | 183/201/297/315/129 |
| Normalized LC elution time * | 1,47 (Kellner 2014) |
| LC elution order/characteristics | between A and m6A (Kellner 2014) |
* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.
LC-MS Publications
| Title | Authors | Journal | Details | ||
|---|---|---|---|---|---|
| Profiling of RNA modifications by multiplexed stable isotope labelling. | Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. | Chem Commun (Camb). | [details] | 24567952 | - |
Comments
Unstable under usual methods of detection, not easily detectable (Glenn Bjork, personal communication). cmo5U (and mcmo5U) is a modification characteristic for gram negative bacteria (E. coli, Protebacteria). Gram positive bacteria (B. subtilis, Firmicutes) have mo5U in this position.
Chemical groups contained
| Type | Subtype |
|---|---|
| other | carboxymethyl |
| other | methoxy |
| other | methylester |
Reactions producing uridine 5-oxyacetic acid methyl ester
| Name |
|---|
| cmo5U:mcmo5U |
Reactions starting from uridine 5-oxyacetic acid methyl ester
| Name |
|---|
| mcmo5U:mcmo5Um |
Publications
| Title | Authors | Journal | Details | ||
|---|---|---|---|---|---|
| The identification of the tRNA substrates for the supK tRNA methylase. | Pope WT, Brown A, Reeves RH | Nucleic Acids Res | [details] | 347399 | - |
Last modification of this entry: Sept. 22, 2023