Modomics - A Database of RNA Modifications

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-methoxycarbonylmethyl-2'-O-methyluridine
IUPAC namemethyl 2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetate
Short namemcm5Um
MODOMICS code new2000090521U
MODOMICS code0521U
Synonyms
1,2,3,4-Tetrahydro-1-(2-O-methyl-beta-D-ribofuranosyl)-2,4-dioxo-5-pyrimidineacetic acid methyl ester
2,3,4-tetrahydropyrimidin-5-yl)acetate
5-(Methoxycarbonyl)methyl-2'-o-methyl uridine
5-methoxycarbonylmethyl-2'-o-methyluridine
60197-31-1
mcm5Um
methyl 2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetate
methyl 2-(1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-2,4-dioxo-1,
Methyl 2-(1-((2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxytetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acetate
MFCD28125310
SCHEMBL2027440
ZINC34363769

Nature of the modified residueNatural
RNAMods code
Residue unique ID80
Found in RNAYes
Related nucleotides361
Found naturally in RNA typestRNA

Chemical information

Sum formulaC13H18N2O8
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2c(=O)[nH]c(=O)c(CC(OC)=O)c2)O[C@H](CO)[C@H]1O
logP-2.4823
TPSA140.08
Number of atoms23
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)3
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/C13H18N2O8/c1-21-8(17)3-6-4-15(13(20)14-11(6)19)12-10(22-2)9(18)7(5-16)23-12/h4,7,9-10,12,16,18H,3,5H2,1-2H3,(H,14,19,20)/t7-,9-,10-,12-/m1/s1
InChIKeyXOTXNXXJZCFUOA-UGKPPGOTSA-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
COC1C(N2C(=O)NC(=O)C(=CC(OC)=O)C2)OC(CO)C1O tautomer #0
COC1C(n2c(=O)[nH]c(=O)c(CC(OC)=O)c2)OC(CO)C1O tautomer #1
COC1C(n2c(=O)[nH]c(=O)c(C=C(OC)O)c2)OC(CO)C1O tautomer #2
COC1C(N2C(O)=NC(=O)C(=CC(OC)=O)C2)OC(CO)C1O tautomer #3
COC1C(n2c(O)nc(=O)c(CC(OC)=O)c2)OC(CO)C1O tautomer #4
COC1C(N2C(=O)N=C(O)C(=CC(OC)=O)C2)OC(CO)C1O tautomer #5
COC1C(n2c(=O)nc(O)c(CC(OC)=O)c2)OC(CO)C1O tautomer #6
COC1C(n2c(O)nc(=O)c(C=C(OC)O)c2)OC(CO)C1O tautomer #7
COC1C(n2c(=O)nc(O)c(C=C(OC)O)c2)OC(CO)C1O tautomer #8

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mcm5Um mcm5Um mcm5Um

* 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 mass330.1063
Average mass330.291
[M+H]+331.1141
Product ions185
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
methyl groupmethyl at O2
othercarboxymethyl
othermethylester

Reactions producing 5-methoxycarbonylmethyl-2'-O-methyluridine

Name
mcm5U:mcm5Um

Reactions starting from 5-methoxycarbonylmethyl-2'-O-methyluridine

Name
mcm5Um:mchm5Um

Last modification of this entry: Sept. 22, 2023