Summary

Full name5-carboxyhydroxymethyluridine
IUPAC name2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]-2-hydroxyacetic acid
Short namechm5U
MODOMICS code520U
Synonyms
5-(carboxy-hydroxymethyl) uridine
5-(carboxyhydroxymethyl)uridine
5-[carboxy(hydroxy)methyl]uridine
CHEBI:20530
chm(5)u
Q27109309
SCHEMBL40819

Nature of the modified residueNatural
RNAMods code
Residue unique ID73
Found in RNAYes
Related nucleotides357

Chemical information

Sum formulaC11H14N2O9
Type of moietynucleoside
Degeneracynot applicable
SMILESOC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(C(C(=O)O)O)c2)O1
logP-3.7339
TPSA182.31
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)6
PDB no exac match , link to the most similar ligand 38T
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000884
InChIInChI=1S/C11H14N2O9/c14-2-4-6(16)7(17)9(22-4)13-1-3(5(15)10(19)20)8(18)12-11(13)21/h1,4-7,9,14-17H,2H2,(H,19,20)(H,12,18,21)/t4-,5?,6-,7-,9-/m1/s1
InChIKeyUVGCZRPOXXYZKH-QADQDURISA-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(C(C(O)=O)=O)C2)O1 tautomer #0
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(C(C(O)O)=O)c2)O1 tautomer #1
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(C(C(O)=O)O)c2)O1 tautomer #2
OCC1C(O)C(O)C(N2C(=O)NC(=O)C(=C(C(O)=O)O)C2)O1 tautomer #3
OCC1C(O)C(O)C(N2C(=O)NC(O)=C(C(C(O)=O)=O)C2)O1 tautomer #4
OCC1C(O)C(O)C(n2c(O)nc(=O)c(C(C(O)O)=O)c2)O1 tautomer #5
OCC1C(O)C(O)C(n2c(O)nc(=O)c(C(C(O)=O)O)c2)O1 tautomer #6
OCC1C(O)C(O)C(N2C(O)=NC(=O)C(C(C(O)=O)=O)C2)O1 tautomer #7
OCC1C(O)C(O)C(n2c(=O)nc(O)c(C(C(O)O)=O)c2)O1 tautomer #8
OCC1C(O)C(O)C(n2c(=O)nc(O)c(C(C(O)=O)O)c2)O1 tautomer #9
OCC1C(O)C(O)C(N2C(=O)N=C(O)C(C(C(O)=O)=O)C2)O1 tautomer #10
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(C(=C(O)O)O)c2)O1 tautomer #11
OCC1C(O)C(O)C(N2C(O)=NC(=O)C(=C(C(O)=O)O)C2)O1 tautomer #12
OCC1C(O)C(O)C(N2C(O)=NC(O)=C(C(C(O)=O)=O)C2)O1 tautomer #13
OCC1C(O)C(O)C(N2C(=O)N=C(O)C(=C(C(O)=O)O)C2)O1 tautomer #14
OCC1C(O)C(O)C(n2c(O)nc(=O)c(C(=C(O)O)O)c2)O1 tautomer #15
OCC1C(O)C(O)C(n2c(=O)nc(O)c(C(=C(O)O)O)c2)O1 tautomer #16

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
chm5U chm5U chm5U

* 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 * 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.

Chemical groups contained

TypeSubtype
othercarboxymethyl
otherhydroxyl

Reactions producing 5-carboxyhydroxymethyluridine

Name
cm5U:chm5U

Reactions starting from 5-carboxyhydroxymethyluridine

Name
chm5U:mchm5U

Last modification of this entry: Sept. 29, 2021


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