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 name5,6-dihydrouridine-5'-monophosphate
IUPAC name[(2R,3S,4R,5R)-5-(2,4-dioxo-1,3-diazinan-1-yl)-3,4-dihydroxyoxolan-2-yl]methyl phosphate
Short namepD
MODOMICS code new2000008551U
MODOMICS code8551U
Synonyms
4g0p
5,6-dihydrouridine 5'-monophosphate
5,6-dihydrouridine 5'-monophosphate(2-)
a 2,4-dioxotetrahydropyrimidine D-ribonucleotide
CHEBI:142106
Nature of the modified residueNatural
RNAMods codeD
Residue unique ID190
Found in RNAYes
Related nucleosides14
RCSB ligands

H2U


Chemical information

Sum formulaC9H13N2O9P
Type of moietynucleotide
Degeneracynot aplicable
SMILES[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C(NC(=O)CC1)=O)(=O)[O-]
logP-1.3726
TPSA181.33
Number of atoms21
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)3
InChIInChI=1S/C9H15N2O9P/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h4,6-8,13-14H,1-3H2,(H,10,12,15)(H2,16,17,18)/p-2/t4-,6-,7-,8-/m1/s1
InChIKeyNBWDKGJHOHJBRJ-XVFCMESISA-L
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
[O-]P(OCC1OC(C(O)C1O)N2C(NC(=O)CC2)=O)(=O)[O-] tautomer #0
[O-]P(OCC1OC(C(O)C1O)N2C(NC(O)=CC2)=O)(=O)[O-] tautomer #1
[O-]P(OCC1OC(C(O)C1O)N2C(=NC(=O)CC2)O)(=O)[O-] tautomer #2
[O-]P(OCC1OC(C(O)C1O)N2C(N=C(O)CC2)=O)(=O)[O-] tautomer #3
[O-]P(OCC1OC(C(O)C1O)N2C(=NC(O)=CC2)O)(=O)[O-] tautomer #4
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
pD pD pD

* 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 massNone
Average mass324.181
[M+H]+ not available
Product ions not available
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.

Last modification of this entry: Sept. 22, 2023