Modomics - A Database of RNA Modifications

Summary

Full name((2S,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-(2- ((((2R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)- 3,4-dihydroxytetrahydrofuran-2-yl)methyl)amino)-2-oxoethyl)-4- hydroxytetrahydrofuran-2-yl)methyl phosphate
IUPAC name[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-[2-[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methylamino]-2-oxoethyl]-4-hydroxyoxolan-2-yl]methyl dihydrogen phosphate
Short nameURU
MODOMICS code 3000000075U
Nature of the modified residueUnnatural
RNAMods code
Residue unique ID264
Found in RNAYes

Chemical information

Sum formulaC20H26N5O14P
Type of moietynucleotide
Degeneracynot aplicable
PubChem ID137350100
SMILES[O-]P(OC[C@H]1O[C@H]([C@H](O)[C@@H]1CC(NC[C@H]1O[C@@H](N2C(=O)NC(=O)C=C2)[C@H](O)[C@@H]1O)=O)N1C(NC(=O)C=C1)=O)(=O)[O-]
logP-4.803899999999993
TPSA284.73
Number of atoms66
Number of Hydrogen Bond Acceptors 1 (HBA1)17
Number of Hydrogen Bond Acceptors 2 (HBA2)17
Number of Hydrogen Bond Donors (HBD)4
InChIInChI=1S/C20H26N5O14P/c26-11-1-3-24(19(32)22-11)17-14(29)8(10(39-17)7-37-40(34,35)36)5-13(28)21-6-9-15(30)16(31)18(38-9)25-4-2-12(27)23-20(25)33/h1-4,8-10,14-18,29-31H,5-7H2,(H,21,28)(H,22,26,32)(H,23,27,33)(H2,34,35,36)/p-2/t8-,9-,10-,14-,15-,16-,17-,18-/m1/s1
InChIKeyWKTKVGCYUSOTBH-VKGBBMGNSA-L
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* 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)C1CC(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)=O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #0

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #1

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)=O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #2

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)=O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #3

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)=O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #4

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #5

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)=O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #6

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #7

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #8

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #9

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #10

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)=O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #11

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)=O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #12

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #13

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #14

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)[nH]c(=O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #15

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)=O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #16

[O-]P(OCC1OC(C(O)C1CC(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)=O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #17

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c([nH]c(=O)cc4)=O)(=O)[O-] tautomer #18

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #19

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #20

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #21

[O-]P(OCC1OC(C(O)C1C=C(NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #22

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #23

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(O)nc(=O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #24

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c(nc(=O)cc4)O)(=O)[O-] tautomer #25

[O-]P(OCC1OC(C(O)C1CC(=NCC2OC(n3c(=O)nc(O)cc3)C(O)C2O)O)n4c(nc(O)cc4)=O)(=O)[O-] tautomer #26


Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
URU URU URU

* 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 mass587.388
[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. 20, 2023