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 namealpha-dimethylmonophosphate 5' cap
Short namemmpN
MODOMICS code new2000002551N
MODOMICS code2551N
Nature of the modified residueNatural
Residue unique ID170
Found in RNAYes
Enzymes BCDIN3D (Homo sapiens)
Found in phylogenyEukaryota
Found naturally in RNA typespre-miRNA

Chemical information

Sum formulaC7H14O7P
Type of moietynucleotide
Degeneracyunspecified residue
Number of atoms16
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)7
Number of Hydrogen Bond Donors (HBD)2
PDB no exac match , link to the most similar ligand N
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

Predicted CYP Metabolic Sites

mmpN mmpN mmpN

* 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 mass320.0062
Average mass241.156
[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.

Chemical groups contained


Reactions producing alpha-dimethylmonophosphate 5' cap



Title Authors Journal Details PubMed Id DOI
Human RNA Methyltransferase BCDIN3D Regulates MicroRNA Processing. Xhemalce B, Robson SC, Kouzarides T... Cell [details] 23063121 -

Last modification of this entry: Sept. 22, 2023