Modomics - A Database of RNA Modifications

mcm5U
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-methoxycarbonylmethyluridine
IUPAC namemethyl 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetate
Short namemcm5U
MODOMICS code new2000000521U
MODOMICS code521U
Synonyms
1,2,3,4-Tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-5-pyrimidineacetic Acid Methyl Ester
29428-50-0
5-(2-methoxy-2-oxoethyl)uridine
5-(2-Oxo-2-methoxyethyl)uridine
5-Mcmu
5-Methoxycarbonyl Methyl Uridine
5-Methoxycarbonylmethyluridine
5-(methoxycarbonyl)methyluridine
5-Pyrimidineacetic acid, 1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofur anosyl-, methyl ester
5-Pyrimidineacetic acid, 1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-, methyl ester
5-Pyrimidineaceticacid, 1,2,3,4-tetrahydro-2,4-dioxo-1-b-D-ribofuranosyl-, methyl ester
5-Pyrimidineaceticacid,1,2,3,4-tetrahydro-2,4-dioxo-1-beta-D-ribofuranosyl-,methylester
AC1MIVNC
C12-H16-N2-O8
C12H16N2O8
CHEBI:20598
CID3080753
DTXSID20183642
imidin-5-yl)acetate
mcm(5)u
mcm5U
methyl 2-[1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetate
methyl 2-(1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyr
Methyl 2-(1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acetate
methyl uridine 5-acetate
Q27109316
SCHEMBL64345
uridine 5-acetic acid methyl ester
YIZYCHKPHCPKHZ-PNHWDRBUSA-N
ZINC33902395
Nature of the modified residueNatural
RNAMods code1
Residue unique ID27
Found in RNAYes
Related nucleotides362
Enzymes ALKBH8 (Homo sapiens)
TRM112 (Homo sapiens)
Trm9 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota
Found naturally in RNA typestRNA

Chemical information

Sum formulaC12H16N2O8
Type of moietynucleoside
Degeneracynot applicable
SMILESCOC(Cc1c(=O)[nH]c(=O)[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1)=O
logP-3.1364
TPSA151.08
Number of atoms22
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)4
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/C12H16N2O8/c1-21-7(16)2-5-3-14(12(20)13-10(5)19)11-9(18)8(17)6(4-15)22-11/h3,6,8-9,11,15,17-18H,2,4H2,1H3,(H,13,19,20)/t6-,8-,9-,11-/m1/s1
InChIKeyYIZYCHKPHCPKHZ-PNHWDRBUSA-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
COC(C=C1C(=O)NC(=O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #0
COC(Cc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #1
COC(=Cc1c(=O)[nH]c(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #2
COC(C=C1C(O)=NC(=O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #3
COC(Cc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #4
COC(C=C1C(=O)N=C(O)N(C2C(O)C(O)C(CO)O2)C1)=O tautomer #5
COC(Cc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)=O tautomer #6
COC(=Cc1c(O)nc(=O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #7
COC(=Cc1c(=O)nc(O)n(C2C(O)C(O)C(CO)O2)c1)O tautomer #8
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
mcm5U mcm5U mcm5U

* 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 mass316.0907
Average mass316.264
[M+H]+317.0985
Product ions185/153/125
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
othermethylester

Reactions producing 5-methoxycarbonylmethyluridine

Name
cm5U:mcm5U

Reactions starting from 5-methoxycarbonylmethyluridine

Name
mcm5U:mchm5U
mcm5U:mcm5s2U
mcm5U:mcm5Um

Publications

Title Authors Journal Details PubMed Id DOI
Biogenesis and growth phase-dependent alteration of 5-methoxycarbonylmethoxyuridine in tRNA anticodons Sakai Y, Miyauchi K, Kimura S, Suzuki T. Nucleic Acids Res. [details] 26681692 10.1093/nar/gkv1470

Last modification of this entry: Sept. 22, 2023