Modomics - A Database of RNA Modifications

mpppN
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

Summary

Full namegamma-methyltriphosphate 5' cap
Short namempppN
MODOMICS code new2000001553N
MODOMICS code1553N
Nature of the modified residueNatural
RNAMods code§
Residue unique ID135
Found in RNAYes
Enzymes MEPCE (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typessnRNA

Chemical information

Sum formulaC6H11O13P3
Type of moietynucleotide
Degeneracyunspecified residue
SMILESCOP([O-])(OP([O-])(OP([O-])(OC[C@H]1O[C@@H]%91[C@H](O)[C@@H]1O)=O)=O)=O.[*]%91
logP0.7143
TPSA236.43
Number of atoms23
Number of Hydrogen Bond Acceptors 1 (HBA1)11
Number of Hydrogen Bond Acceptors 2 (HBA2)13
Number of Hydrogen Bond Donors (HBD)2
PDB no exac match , link to the most similar ligand CU0
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
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
mpppN mpppN mpppN

* 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 mass172.9405
Average mass384.065
[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.

Comments

See 'Modification and Editing of RNA', edited by Henri Grosjean; chapter 11.

Chemical groups contained

TypeSubtype
otherother

Reactions producing gamma-methyltriphosphate 5' cap

Name
pppN:mpppN

Last modification of this entry: Sept. 22, 2023