Summary

Full nameuridine 5-oxyacetic acid
IUPAC name2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]oxyacetic acid
Short namecmo5U
MODOMICS code502U
Synonyms
2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]oxyacetic acid
2-((1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)oxy)acetic acid
28144-25-4
33863-77-3
5-(carboxymethoxy)uridine
5-oxyacetyluridine
AC1L4VKW
AC1Q5WPL
Acetic acid, ((1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-5-pyrimidinyl)oxy)-
Acetic acid,2-[(1,2,3,4-tetrahydro-2,4-dioxo-1-b-D-ribofuranosyl-5-pyrimidinyl)oxy]-
AR-1G5490
CHEBI:27240
CID193091
CTK4G0918
DTXSID80182414
J-016986
o(5)u
Q27109940
SCHEMBL41703
uridin-5-yloxyacetic acid
Uridine-5-oxyacetic acid

Nature of the modified residueNatural
RNAMods codeV
Residue unique ID47
Found in RNAYes
Related nucleotides241
Enzymes CmoB (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC11H14N2O9
Type of moietynucleoside
Degeneracynot applicable
PubChem ID193091
SMILESOC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(OCC(=O)O)c2)O1
logP-3.3885
TPSA171.31
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)5
PDB no exac match , link to the most similar ligand CM0
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C11H14N2O9/c14-2-5-7(17)8(18)10(22-5)13-1-4(21-3-6(15)16)9(19)12-11(13)20/h1,5,7-8,10,14,17-18H,2-3H2,(H,15,16)(H,12,19,20)/t5-,7-,8-,10-/m1/s1
InChIKeyRVCNQQGZJWVLIP-VPCXQMTMSA-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
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(OCC(O)=O)c2)O1 tautomer #0
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(OC=C(O)O)c2)O1 tautomer #1
OCC1C(O)C(O)C(n2c(O)nc(=O)c(OCC(O)=O)c2)O1 tautomer #2
OCC1C(O)C(O)C(n2c(=O)nc(O)c(OCC(O)=O)c2)O1 tautomer #3
OCC1C(O)C(O)C(n2c(O)nc(=O)c(OC=C(O)O)c2)O1 tautomer #4
OCC1C(O)C(O)C(n2c(=O)nc(O)c(OC=C(O)O)c2)O1 tautomer #5

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
cmo5U cmo5U cmo5U

* 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 mass318.0699
Average mass318.237
[M+H]+319.0777
Product ions187/169/141
Normalized LC elution time *0,54 (Kellner 2014)
LC elution order/characteristicsbetween C and U (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 PubMed Id DOI
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

Earlier called the V nucleoside. Base pairs with A, G and U in mRNA. 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

TypeSubtype
othercarboxymethyl
othermethoxy

Reactions producing uridine 5-oxyacetic acid

Name
ho5U:cmo5U
mo5U:cmo5U

Reactions starting from uridine 5-oxyacetic acid

Name
cmo5U:mcmo5U

Publications

Title Authors Journal Details PubMed Id DOI
The wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of G-ending codons. Nasvall SJ, Chen P, Bjork GR RNA [details] 17942742 -
Uridin-5-oxy acetic acid: a new minor constituent from E. coli valine transfer RNA I. Murao K, Saneyoshi M, Harada F, Nishimura S Biochem Biophys Res Commun [details] 4910247 -

Last modification of this entry: Sept. 29, 2021


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