Modomics - A Database of RNA Modifications

pG2'3'cp
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 nameguanoside-5'-phosphate-2',3'-cyclic phosphate
Short namepG2'3'cp
MODOMICS code new2000003377G
MODOMICS code3377G
Nature of the modified residueNatural
Residue unique ID238
Found in RNAYes
Related nucleosides38
RCSB ligands

23G


Chemical information

Sum formulaC10H9N5O10P2
Type of moietynucleotide
Degeneracynot aplicable
SMILES[C@H]1([n]2cnc3c2nc(nc3=O)N)[C@@H]2O[P@]([O-])(=O)O[C@@H]2[C@@H](COP([O-])([O-])=O)O1
logP-1.9061
TPSA243.27
Number of atoms27
Number of Hydrogen Bond Acceptors 1 (HBA1)12
Number of Hydrogen Bond Acceptors 2 (HBA2)15
Number of Hydrogen Bond Donors (HBD)1
InChIInChI=1S/C10H12N5O10P2/c11-10-13-7-4(8(16)14-10)12-2-15(7)9-6-5(24-27(20,21)25-6)3(23-9)1-22-26(17,18)19/h2-3,5-6,9H,1H2,(H,20,21)(H2,11,14,16)(H2,17,18,19)/p-3/t3-,5-,6-,9-/m1/s1
InChIKeyMYDHAVOCUFAOHX-UUOKFMHZSA-K
Search the molecule in external databases ChEMBL  PubChem Compound Database  Ligand Expo  WIPO 

* 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]:29.966535453
Energy [Eh]:-2095.69348519787
HOMO [eV]:-8.3322
LUMO [eV]:1.5068
Gap [eV]:9.839

Download QM Data:

Charges   charge.txt

Download Structures

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


LC-MS Information

Monoisotopic massNone
Average mass421.153
[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. 15, 2025