Modomics - A Database of RNA Modifications

cm5U
The molecule is shown in a ball-and-stick representation with the following colors for atoms :
⬤ Hydrogen (H): white ⬤ Carbon (C): gray ⬤ Oxygen (O): red ⬤ Phosphorus (P): orange ⬤ Nitrogen (N): blue ⬤ Selenium (Se): gold ⬤ Sulfur (S): yellow

Summary

Full name5-carboxymethyluridine
IUPAC name2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetic acid
Short namecm5U
MODOMICS code new2000000052U
MODOMICS code52U
Synonyms
1-(beta-D-ribofuranosyl)-5-(carboxymethyl)uracil
20964-06-1
2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetic 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)acetic acid
2-(1-((2S,3S,4R,5S)-3,4-dihydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acetic acid?AC1MIVKU; SureCN157985; AG-E-53883
2,4-dioxo-1-beta-D-ribofuranosyl-1,2,3,4-tetrahydropyrimidin-5-ylacetic acid
5-Carboxymethyluridine
5-(carboxymethyl)uridine
5-Carboxymethyl-uridine; LC-tDDA; CE10
5-Pyrimidineacetic acid, 1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-
AC1MIVKU
CHEBI:75654
CID3080720
CTK4E5555
DTXSID20175143
N/A
Q27145450
SCHEMBL157985
Uridine-5-acetic acid
Nature of the modified residueNatural
RNAMods code◊
Residue unique ID44
Found in RNAYes
Related nucleotides359
Found in phylogenyEukaryota

Chemical information

Sum formulaC11H14N2O8
Type of moietynucleoside
Degeneracynot applicable
PubChem ID3080720
SMILESOC[C@@H]1[C@@H](O)[C@@H](O)[C@H]([n]2c(=O)[nH]c(=O)c(CC(=O)O)c2)O1
logP-3.2248
TPSA162.08
Number of atoms21
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand 38T
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C11H14N2O8/c14-3-5-7(17)8(18)10(21-5)13-2-4(1-6(15)16)9(19)12-11(13)20/h2,5,7-8,10,14,17-18H,1,3H2,(H,15,16)(H,12,19,20)/t5-,7-,8-,10-/m1/s1
InChIKeyFAWQJBLSWXIJLA-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(CC(O)=O)c2)O1 tautomer #0
OCC1C(O)C(O)C(N2C(=O)NC(=O)C(=CC(O)=O)C2)O1 tautomer #1
OCC1C(O)C(O)C(n2c(=O)[nH]c(=O)c(C=C(O)O)c2)O1 tautomer #2
OCC1C(O)C(O)C(n2c(O)nc(=O)c(CC(O)=O)c2)O1 tautomer #3
OCC1C(O)C(O)C(N2C(O)=NC(=O)C(=CC(O)=O)C2)O1 tautomer #4
OCC1C(O)C(O)C(n2c(=O)nc(O)c(CC(O)=O)c2)O1 tautomer #5
OCC1C(O)C(O)C(N2C(=O)N=C(O)C(=CC(O)=O)C2)O1 tautomer #6
OCC1C(O)C(O)C(n2c(O)nc(=O)c(C=C(O)O)c2)O1 tautomer #7
OCC1C(O)C(O)C(n2c(=O)nc(O)c(C=C(O)O)c2)O1 tautomer #8
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
cm5U cm5U cm5U

* 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 mass302.075
Average mass302.237
[M+H]+303.0828
Product ions171
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.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry. Su D, Chan CT, Gu C, Lim KS, Chionh YH, McBee ME, Russell BS, Babu IR, Begley TJ, Dedon PC... Nat Protoc [details] 24625781 -

Chemical groups contained

TypeSubtype
othercarboxymethyl

Reactions producing 5-carboxymethyluridine

Name
U:cm5U

Reactions starting from 5-carboxymethyluridine

Name
cm5U:mcm5U
cm5U:chm5U

Last modification of this entry: Sept. 22, 2023