Summary

Full name5-methyldihydrouridine
IUPAC name1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-diazinane-2,4-dione
Short namem5D
MODOMICS code58U
Synonyms
1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-diazinane-2,4-dione
1-((2R,3R,4S,5R)-3,4-Dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methyldihydropyrimidine-2,4(1H,3H)-dione
1463-10-1
23067-10-9
5,6-Dihydro-5-methyluridine
5-Methyl-5,6-dihydrouridine
5-methyldihydrouridine
5-Methyluridine
CS-0114106
CTK4F0814
DIHYDRORIBOSYLTHYMINE
DTXSID00617899
HY-130803
MFCD09842115
N/A
Ribothymidine
RTR-005799
SCHEMBL1964824
TR-005799
Uridine, 5,6-dihydro-5-methyl-
Uridine, 5-methyl-

Nature of the modified residueNatural
RNAMods codeρ
Residue unique ID17
Found in RNAYes
Related nucleotides364

Chemical information

Sum formulaC10H16N2O6
Type of moietynucleoside
Degeneracynot applicable
SMILESCC1C(=O)NC(=O)N([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)C1
logP-2.12
TPSA119.33
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)8
Number of Hydrogen Bond Donors (HBD)4
PDB no exac match , link to the most similar ligand 5HT
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000497
InChIInChI=1S/C10H16N2O6/c1-4-2-12(10(17)11-8(4)16)9-7(15)6(14)5(3-13)18-9/h4-7,9,13-15H,2-3H2,1H3,(H,11,16,17)/t4?,5-,6-,7-,9-/m1/s1
InChIKeyBTFXIEGOSDSOGN-KWCDMSRLSA-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
CC1C(=O)NC(=O)N(C2C(O)C(O)C(CO)O2)C1 tautomer #0
CC1=C(O)NC(=O)N(C2C(O)C(O)C(CO)O2)C1 tautomer #1
CC1C(=O)N=C(O)N(C2C(O)C(O)C(CO)O2)C1 tautomer #2
CC1C(O)=NC(=O)N(C2C(O)C(O)C(CO)O2)C1 tautomer #3
CC1=C(O)N=C(O)N(C2C(O)C(O)C(CO)O2)C1 tautomer #4

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
m5D m5D m5D

* 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 mass260.1008
Average mass260.244
[M+H]+261.1086
Product ions129
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 aliphatic C
ring modificationpartial saturation

Reactions producing 5-methyldihydrouridine

Name
D:m5D

Last modification of this entry: Sept. 29, 2021


Copyright © Genesilico - All rights reserved
If you have any advice or suggestions for corrections or improvements, please contact: Andrea Cappannini - lp.vog.bcmii@ininnappaca