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


Full nameN7-methyl-guanosine cap (cap 0)
Short namem7GpppN
MODOMICS code new2000079553N
MODOMICS code79553N
Nature of the modified residueNatural
RNAMods code©
Residue unique ID132
Found in RNAYes
Enzymes Abd1 (Saccharomyces cerevisiae)
Hcm1 (Homo sapiens)
TRM112 (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typesmRNA, snRNA

Chemical information

Sum formulaC16H23N5O17P3
Type of moietynucleotide
Degeneracyunspecified residue
Number of atoms42
Number of Hydrogen Bond Acceptors 1 (HBA1)17
Number of Hydrogen Bond Acceptors 2 (HBA2)20
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand GTG
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None

* 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
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c([nH]c(=N)[nH]4)=O tautomer #0
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c([nH]c(N)n4)=O tautomer #1
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c(nc(N)n4)O tautomer #2
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c(nc(N)[nH]4)=O tautomer #3
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c([nH]c(=N)n4)O tautomer #4
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c(nc(N)n4)O tautomer #5
C[N+]1=CN(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)C=4C1C(NC(=N)N4)=O tautomer #6
C[n+]1cn(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)c4c1c(nc(=N)[nH]4)O tautomer #7
C[N+]1=CN(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)C=4C1C(N=C(N)N4)=O tautomer #8
C[N+]1=CN(C2OC(COP([O-])(OP([O-])(OP([O-])(OCC3OC(C(O)C3O)*)=O)=O)=O)C(O)C2O)C=4C1C(=NC(=N)N4)O tautomer #9

Tautomer image Show Image

Predicted CYP Metabolic Sites

m7GpppN m7GpppN m7GpppN

* 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 mass455.0243
Average mass650.298
[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.


wikipedia: The 5' cap is found on the 5' end of an mRNA molecule and consists of a guanine nucleotide connected to the mRNA via an unusual 5' to 5' triphosphate linkage. This guanosine is methylated on the 7 position directly after capping in vitro by a methyl transferase. It is referred to as a 7-methylguanosine cap, abbreviated m7G. Most properties, save the triphosphate linkage, are the same as any other 7-methylguanosine.

Chemical groups contained

methyl groupmethyl group

Reactions producing N7-methyl-guanosine cap (cap 0)


Reactions starting from N7-methyl-guanosine cap (cap 0)


Last modification of this entry: Sept. 22, 2023