Summary

Full name[(2~{R},3~{R},4~{R},5~{R})-5-(4-acetamido-2-oxidanylidene-pyrimidin-1-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
Short namepac4Cm
MODOMICS code042551C
Nature of the modified residueNatural
Residue unique ID257
Found in RNAYes
Related nucleosides106
RCSB ligands

LHH


Chemical information

Sum formulaC12H16N3O9P
Type of moietynucleotide
Degeneracynot aplicable
SMILESCO[C@H]1[C@H]([n]2c(=O)nc(NC(=O)C)cc2)O[C@H](COP(=O)([O-])[O-])[C@H]1O
logP-0.4663
TPSA184.91
Number of atoms25
Number of Hydrogen Bond Acceptors 1 (HBA1)9
Number of Hydrogen Bond Acceptors 2 (HBA2)12
Number of Hydrogen Bond Donors (HBD)2
InChIInChI=1S/C12H18N3O9P/c1-6(16)13-8-3-4-15(12(18)14-8)11-10(22-2)9(17)7(24-11)5-23-25(19,20)21/h3-4,7,9-11,17H,5H2,1-2H3,(H2,19,20,21)(H,13,14,16,18)/p-2/t7-,9-,10-,11-/m1/s1
InChIKeyXSIWUOJELZFTTR-QCNRFFRDSA-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
COC1C(n2c(=O)[nH]c(=NC(=O)C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #0
COC1C(n2c(=O)nc(NC(=O)C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #1
COC1C(n2c(=O)[nH]c(=NC(O)=C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #2
COC1C(n2c(=O)nc(NC(O)=C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #3
COC1C(n2c(O)nc(=NC(=O)C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #4
COC1C(n2c(=O)nc(N=C(O)C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #5
COC1C(n2c(O)nc(=NC(O)=C)cc2)OC(COP(=O)([O-])[O-])C1O tautomer #6

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
pac4Cm pac4Cm pac4Cm

* 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 mass377.244
[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. 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