Summary

Full name5' diphosphate end
Short nameppN
MODOMICS code552N
Nature of the modified residueNatural
RNAMods codeϒ
Residue unique ID153
Found in RNAYes
Enzymes Cet1 (Saccharomyces cerevisiae)
HCAP1 (Homo sapiens)
Found in phylogenyEukaryota

Chemical information

Sum formulaC5H8O10P2
Type of moietynucleotide
Degeneracyunspecified residue
SMILESO[C@H]1[C@H]%91O[C@H](COP(OP(=O)([O-])[O-])(=O)[O-])[C@H]1O.[*]%91
logP-0.0568
TPSA191.09
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)10
Number of Hydrogen Bond Donors (HBD)2
PDB no exac match , link to the most similar ligand CU0
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0060500
InChI
InChIKey

* 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


Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ppN ppN ppN

* 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 mass78.9585
Average mass290.059
[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.

Reactions producing 5' diphosphate end

Name
pppN:ppN

Reactions starting from 5' diphosphate end

Name
ppN:GpppN

Last modification of this entry: Sept. 29, 2021


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