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-carbamoylmethyl-2'-O-methyluridine
IUPAC name2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetamide
Short namencm5Um
MODOMICS code new2000009053U
MODOMICS code053U
Synonyms
2-[1-[(2R,3R,4R,5R)-4-hydroxy-5-(hydroxymethyl)-3-methoxyoxolan-2-yl]-2,4-dioxopyrimidin-5-yl]acetamide
4-Hydroxy-5-(2-hydroxy-2-iminoethyl)-1-(2-O-methylpentofuranosyl)pyrimidin-2(1H)-one
5-(2-amino-2-oxoethyl)-2'-o-methyluridine
5-carbamoylmethyl-2'-o-methyluridine
60197-30-0
6635-88-7
AC1L4XLB
AC1Q5J6E
AR-1G4978
CID194102
DTXSID30975616
O(2)'-Methyl-5-carbamoylmethyluridine
SCHEMBL992387
Uridine, 5-(2-amino-2-oxoethyl)-2'-O-methyl-

Nature of the modified residueNatural
RNAMods code~
Residue unique ID29
Found in RNAYes
Related nucleotides389
Enzymes Trm7 (Saccharomyces cerevisiae)

Chemical information

Sum formulaC12H17N3O7
Type of moietynucleoside
Degeneracynot applicable
SMILESCO[C@H]1[C@H]([n]2cc(CC(N)=O)c(=O)[nH]c2=O)O[C@H](CO)[C@H]1O
logP-2.4697
TPSA156.87
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/C12H17N3O7/c1-21-9-8(18)6(4-16)22-11(9)15-3-5(2-7(13)17)10(19)14-12(15)20/h3,6,8-9,11,16,18H,2,4H2,1H3,(H2,13,17)(H,14,19,20)/t6-,8-,9-,11-/m1/s1
InChIKeyVHXUHQJRMXUOST-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
COC1C(n2cc(CC(N)=O)c(=O)[nH]c2=O)OC(CO)C1O tautomer #0
COC1C(N2CC(=CC(N)=O)C(=O)NC2=O)OC(CO)C1O tautomer #1
COC1C(n2cc(C=C(N)O)c(=O)[nH]c2=O)OC(CO)C1O tautomer #2
COC1C(n2cc(CC(N)=O)c(O)nc2=O)OC(CO)C1O tautomer #3
COC1C(n2cc(CC(N)=O)c(=O)nc2O)OC(CO)C1O tautomer #4
COC1C(N2CC(=CC(N)=O)C(O)=NC2=O)OC(CO)C1O tautomer #5
COC1C(N2CC(=CC(N)=O)C(=O)N=C2O)OC(CO)C1O tautomer #6
COC1C(N2CC(=CC(=N)O)C(=O)NC2=O)OC(CO)C1O tautomer #7
COC1C(n2cc(CC(=N)O)c(=O)[nH]c2=O)OC(CO)C1O tautomer #8
COC1C(n2cc(C=C(N)O)c(O)nc2=O)OC(CO)C1O tautomer #9
COC1C(n2cc(C=C(N)O)c(=O)nc2O)OC(CO)C1O tautomer #10
COC1C(N2CC(=CC(=N)O)C(O)=NC2=O)OC(CO)C1O tautomer #11
COC1C(N2CC(=CC(=N)O)C(=O)N=C2O)OC(CO)C1O tautomer #12
COC1C(n2cc(CC(=N)O)c(O)nc2=O)OC(CO)C1O tautomer #13
COC1C(n2cc(CC(=N)O)c(=O)nc2O)OC(CO)C1O tautomer #14

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ncm5Um ncm5Um ncm5Um

* 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 mass315.1066
Average mass315.279
[M+H]+316.1144
Product ions170/153/125
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.

Chemical groups contained

TypeSubtype
methyl groupmethyl at O2
methyl groupmethyl at aromatic C
othercarbamoyl

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

Name
ncm5U:ncm5Um

Last modification of this entry: Sept. 22, 2023