Summary

Full name5-hydroxyuridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxypyrimidine-2,4-dione
Short nameho5U
MODOMICS code50U
Synonyms
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxypyrimidine-2,4-dione
1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-hydroxypyrimidine-2,4(1H,3H)-dione
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-5-hydroxy-pyrimidine-2,4-dione
1-(beta-D-ribofuranosyl)-5-hydroxypyrimidine-2,4(1H,3H)-dione
2,4(1H,3H)-Pyrimidinedione, 5-hydroxy-1-.beta.-D-ribofuranosyl-
36675-91-9
4,5-dihydroxy-1-pentofuranosylpyrimidin-2(1H)-one
5-Hydroxyuridine
5-Oxouridine
957-77-7
AC1L3RPQ
C9-H12-N2-O7
C9H12N2O7
CHEBI:149645
CID94196
CJ-28906
CTK5H8174
DTXSID60914856
EINECS 213-487-1
Isobarbituric acid, 1-.beta.-D-ribofuranosyl-
isobarbituridine
MFCD00010571
NS00042468
NSC73376
SCHEMBL451947
Uridine, 5-hydroxy-
Uridine,5-hydroxy-
ZINC1707733

Nature of the modified residueNatural
RNAMods code
Residue unique ID64
Found in RNAYes
Related nucleotides360
Found in phylogenyEubacteria

Chemical information

Sum formulaC9H12N2O7
Type of moietynucleoside
Degeneracynot applicable
SMILESOC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(O)c2)O1
logP-3.1463
TPSA145.01
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)7
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand URI
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000296
InChIInChI=1S/C9H12N2O7/c12-2-4-5(14)6(15)8(18-4)11-1-3(13)7(16)10-9(11)17/h1,4-6,8,12-15H,2H2,(H,10,16,17)/t4-,5-,6-,8-/m1/s1
InChIKeyQXDXBKZJFLRLCM-UAKXSSHOSA-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)NC(=O)C(=O)C2)O1 tautomer #0
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(O)c2)O1 tautomer #1
OCC1C(O)C(O)C(N2C(O)=NC(=O)C(=O)C2)O1 tautomer #2
OCC1C(O)C(O)C(N2C(=O)N=C(O)C(=O)C2)O1 tautomer #3
OCC1C(O)C(O)C(n2c(O)nc(=O)c(O)c2)O1 tautomer #4
OCC1C(O)C(O)C(n2c(=O)nc(O)c(O)c2)O1 tautomer #5

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ho5U ho5U ho5U

* 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 mass260.0645
Average mass260.201
[M+H]+261.0717
Product ions129
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

ho5U at the wobble position of bacterial tRNA has been demonstrated in null-mutation CmoB. Null mutation of CmoA in S. enterica results in the accummulation of tRNA containing mo5U34 and ho5U34.

Chemical groups contained

TypeSubtype
otherhydroxyl

Reactions producing 5-hydroxyuridine

Name
U:ho5U

Reactions starting from 5-hydroxyuridine

Name
ho5U:cmo5U
ho5U:mo5U
ho5U:mo5U

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 -
Isolation of 5-hydroxyuridine (iso-barbituridine) from yeast ribonucleic acids. Lis AW, Passarge WE Arch Biochem Biophys [details] 5957714 -

Last modification of this entry: Sept. 29, 2021


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