Summary

Full name1-methylpseudouridine
IUPAC name5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methylpyrimidine-2,4-dione
Short namem1Y
MODOMICS code19U
Synonyms
09RAD4M6WF
13860-38-3
1-methyl-pseudouridine
1-Methylpseudouridine
1-N-Methyl-pseudouridine
(1S)-1,4-anhydro-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol
2,4(1H,3H)-Pyrimidinedione, 1-methyl-5-beta-D-ribofuranosyl-
2,4(1H,3H)-Pyrimidinedione,1-methyl-5-b-D-ribofuranosyl-
5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methylpyrimidine-2,4-dione
5-((2S,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-1-methylpyrimidine-2,4(1H,3H)-dione
AC1L40YV
AKOS030241474
C10-H14-N2-O6
CHEBI:19068
CID99543
CS-0047598
CTK4C1317
DTXSID50160724
HY-112582
m(1)f
MFCD10687017
N1-methyl-pseudouridine
N1-Methylpseudouridine
NSC 240023
Q27109108
SCHEMBL63879
U-50228
UNII-09RAD4M6WF
ZINC6072377

Nature of the modified residueNatural
RNAMods code]
Residue unique ID88
Found in RNAYes
Related nucleotides345
Enzymes Nep1 (Saccharomyces cerevisiae)
Nep1 (Methanocaldococcus jannaschii)
TrmY (Haloferax volcanii)
TrmY (Methanocaldococcus jannaschii)
Found in phylogenyArchaea, Eukaryota
Found naturally in RNA typesrRNA, tRNA

Chemical information

Sum formulaC10H14N2O6
Type of moietynucleoside
Degeneracynot applicable
SMILESC[n]1c(=O)[nH]c(=O)c([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)c1
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/c1-12-2-4(9(16)11-10(12)17)8-7(15)6(14)5(3-13)18-8/h2,5-8,13-15H,3H2,1H3,(H,11,16,17)/t5-,6-,7-,8+/m1/s1
InChIKeyUVBYMVOUBXYSFV-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)[nH]c(=O)c(C2C(O)C(O)C(CO)O2)c1 tautomer #0
Cn1c(O)nc(=O)c(C2C(O)C(O)C(CO)O2)c1 tautomer #1
Cn1c(=O)nc(O)c(C2C(O)C(O)C(CO)O2)c1 tautomer #2

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m1Y m1Y m1Y

* 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 1-methylpseudouridine

Name
Y:m1Y

Reactions starting from 1-methylpseudouridine

Name
m1Y:m1acp3Y

Last modification of this entry: Sept. 29, 2021


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