Modomics - A Database of RNA Modifications


Full nameguanosine triphosphate 5' cap (cap G)
Short nameGpppN
MODOMICS code9553N
Nature of the modified residueNatural
RNAMods codeϑ
Residue unique ID148
Found in RNAYes
Enzymes Ceg1 (Saccharomyces cerevisiae)
HCAP1 (Homo sapiens)
Found in phylogenyEukaryota

Chemical information

Sum formulaC15H20N5O17P3
Type of moietynucleotide
Degeneracyunspecified residue
Number of atoms41
Number of Hydrogen Bond Acceptors 1 (HBA1)18
Number of Hydrogen Bond Acceptors 2 (HBA2)21
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand G5J
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0001273

* 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 SMILES
N=c1[nH]c(=O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)[nH]1 tautomer #0
Nc1[nH]c(=O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)n1 tautomer #1
Nc1nc(O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)n1 tautomer #2
Nc1nc(=O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)[nH]1 tautomer #3
N=c1[nH]c(O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)n1 tautomer #4
Nc1nc(O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)n1 tautomer #5
N=C1NC(=O)C2C(N(C=N2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)=N1 tautomer #6
N=c1nc(O)c2c(n(cn2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)[nH]1 tautomer #7
NC1=NC(=O)C2C(N(C=N2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)=N1 tautomer #8
N=C1N=C(O)C2C(N(C=N2)C3OC(COP([O-])(OP([O-])(OP([O-])(OCC4OC(C(O)C4O)*)=O)=O)=O)C(O)C3O)=N1 tautomer #9

Tautomer image Show Image

Predicted CYP Metabolic Sites

GpppN GpppN GpppN

* 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 mass440.0008
Average mass635.264
[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 triphosphate 5' cap (cap G)


Reactions starting from guanosine triphosphate 5' cap (cap G)


Last modification of this entry: Sept. 29, 2021

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