Summary

Full name3-methylpseudouridine
IUPAC name5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-methyl-1H-pyrimidine-2,4-dione
Short namem3Y
MODOMICS code39U
Synonyms
2,4(1H,3H)-Pyrimidinedione, 3-methyl-5-beta-D-ribofuranosyl-
2,4(1H,3H)-Pyrimidinedione,3-methyl-5-b-D-ribofuranosyl-
3-Methyl-5-(beta-D-ribofuranosyl)uracil
3-Methylpseudouridine
3-METHYLPSEUDOURIDINE; NSC 363818
5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-3-methyl-1H-pyrimidine-2,4-dione
81691-06-7
CID11207624
CTK5E9006
NSC 363818
SCHEMBL1964384

Nature of the modified residueNatural
RNAMods codeκ
Residue unique ID48
Found in RNAYes
Related nucleotides349
Enzymes RlmH (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typesrRNA

Chemical information

Sum formulaC10H14N2O6
Type of moietynucleoside
Degeneracynot applicable
SMILESC[n]1c(=O)c([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c[nH]c1=O
logP-2.7724
TPSA124.78
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)6
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 5MD
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000767
InChIInChI=1S/C10H14N2O6/c1-12-9(16)4(2-11-10(12)17)8-7(15)6(14)5(3-13)18-8/h2,5-8,13-15H,3H2,1H3,(H,11,17)/t5-,6-,7-,8+/m1/s1
InChIKeyDXEJZRDJXRVUPN-XUTVFYLZSA-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
CN1C(=O)C(C2C(O)C(O)C(CO)O2)C=NC1=O tautomer #0
Cn1c(=O)c(C2C(O)C(O)C(CO)O2)c[nH]c1=O tautomer #1
Cn1c(O)c(C2C(O)C(O)C(CO)O2)cnc1=O tautomer #2
Cn1c(=O)c(C2C(O)C(O)C(CO)O2)cnc1O tautomer #3

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m3Y m3Y m3Y

* 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 mass258.0852
Average mass258.228
[M+H]+259.093
Product ions169/179/227/209
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 aromatic N
ring modificationpseudouridine

Reactions producing 3-methylpseudouridine

Name
Y:m3Y

Last modification of this entry: Sept. 29, 2021


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