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
See the molecule on the similarity map

Summary

Full nameguanosine added to any ribonucleotide
Short namepG(pN)
MODOMICS code new2000000551G2000000511N
MODOMICS code551G551N
Nature of the modified residueNatural
Residue unique ID161
Found in RNAYes
Enzymes Thg1 (Saccharomyces cerevisiae)
Found in phylogenyEukaryota

Chemical information

Sum formulaC15H19N5O14P2
Type of moietynucleotide
Degeneracyunspecified residue
SMILESNc1[nH]c2c(nc[n]2[C@H]2[C@H](O)[C@H](OP(OC[C@@H]3[C@@H](O)[C@@H](O)[C@H]%91O3)(=O)[O-])[C@@H](COP(=O)([O-])[O-])O2)c(=O)n1.[*]%91
logP-1.1167
TPSA319.37
Number of atoms37
Number of Hydrogen Bond Acceptors 1 (HBA1)15
Number of Hydrogen Bond Acceptors 2 (HBA2)18
Number of Hydrogen Bond Donors (HBD)5
InChINone
InChIKeyNone

* Chemical properties calculated with Open Babel - O'Boyle et al. Open Babel: An open chemical toolbox. J Cheminform 3, 33 (2011) (link)

QM Data:

Dipole Magnitude [D]:None
Energy [Eh]:None
HOMO [eV]:-7.4695
LUMO [eV]:-1.4993
Gap [eV]:5.9702

Download QM Data:

Cube   .cube
Charges   charge.txt

Download Structures

2D   .png .mol .mol2 .sdf .pdb .smi
3D   .mol .mol2 .sdf .pdb

Tautomers

Tautomers SMILES
N=c1[nH]c2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(=O)[nH]1 tautomer #0
Nc1nc2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(=O)[nH]1 tautomer #1
Nc1nc2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(O)n1 tautomer #2
Nc1[nH]c2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(=O)n1 tautomer #3
N=c1nc2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(O)[nH]1 tautomer #4
Nc1nc2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(O)n1 tautomer #5
N=C1N=C2C(N=CN2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)C(=O)N1 tautomer #6
N=c1[nH]c2c(ncn2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)c(O)n1 tautomer #7
NC=1N=C2C(N=CN2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)C(=O)N1 tautomer #8
N=C1N=C2C(N=CN2C3C(O)C(OP(OCC4C(O)C(O)C(O4)*)(=O)[O-])C(COP(=O)([O-])[O-])O3)C(O)=N1 tautomer #9
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
pG(pN) pG(pN) pG(pN)

* 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 mass362.0502
Average mass555.284
[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 guanosine added to any ribonucleotide

Name
pN:pG(pN)

Last modification of this entry: Sept. 15, 2025