Summary

Full nameuridine
Short nameU
MODOMICS codeU
Nature of the modified residueNatural
RNAMods codeU
Residue unique ID60
Found in RNAYes
Related nucleotides255
Enzymes CDAT8 (Methanopyrus kandleri)
Found in phylogenyArchaea, Eubacteria, Eukaryota
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC9H12N2O6
Type of moietynucleoside
Degeneracynot applicable
PubChem ID6029
SMILESOC[C@H]1O[C@@H]([n]2ccc(=O)[nH]c2=O)[C@H](O)[C@@H]1O
logP-2.8519
TPSA124.78
Number of atoms17
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand URI
PDB exact match , link to the most similar ligand URI
HMDB (Human Metabolome Database) exact match HMDB0000296
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChIKeyDRTQHJPVMGBUCF-XVFCMESISA-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
OCC1OC(n2ccc(=O)[nH]c2=O)C(O)C1O tautomer #0
OCC1OC(n2ccc(=O)nc2O)C(O)C1O tautomer #1
OCC1OC(n2ccc(O)nc2=O)C(O)C1O tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
U U U

* 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 mass244.0695
Average mass244.201
[M+H]+245.0773
Product ions113
Normalized LC elution time *0.58
LC elution order/characteristics not available

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.

Reactions producing uridine

Name
C:U

Reactions starting from uridine

Name
U:acp3U
U:Um
U:cm5U
U:m3U
U:ho5U
U:ncm5U
U:D
U:Y
U:s2U
U:s4U
U:m5U
U:nm5U
U:cmnm5U
U:tm5U

Last modification of this entry: Sept. 29, 2021


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