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 nameagmatidine
IUPAC name2-[4-[[4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-ylidene]amino]butyl]guanidine
Short nameC+
MODOMICS code new2000000020C
Nature of the modified residueNatural
RNAMods code¿
Residue unique ID141
Found in RNAYes
Related nucleotides411
Enzymes TiaS (Archaeoglobus fulgidus)
Found in phylogenyArchaea
Found naturally in RNA typestRNA

Chemical information

Sum formulaC14H25N7O4
Type of moietynucleoside
Degeneracynot applicable
Number of atoms25
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)8
PDB no exac match , link to the most similar ligand JMH
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 
PubChem CID
PubChem SIDs

* 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
NC(=NCCCCN=c1nc(N)ccn1C2OC(CO)C(O)C2O)N tautomer #0
NC(NCCCCN=c1nc(N)ccn1C2OC(CO)C(O)C2O)=N tautomer #1
NC(=NCCCCNc1nc(=N)ccn1C2OC(CO)C(O)C2O)N tautomer #2
NC(=NCCCCN=c1[nH]c(=N)ccn1C2OC(CO)C(O)C2O)N tautomer #3
NC(NCCCCNc1nc(=N)ccn1C2OC(CO)C(O)C2O)=N tautomer #4
NC(NCCCCN=c1[nH]c(=N)ccn1C2OC(CO)C(O)C2O)=N tautomer #5
Tautomer image Show Image

Predicted CYP Metabolic Sites

C+ C+ C+

* 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 mass355.1968
Average mass355.393
Product ions224
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.


alternative name: 2-agmatinylcytidine, alternative abbreviation: agmt

Reactions producing agmatidine



Title Authors Journal Details PubMed Id DOI
Agmatidine, a modified cytidine in the anticodon of archaeal tRNA(Ile), base pairs with adenosine but not with guanosine. Mandal D, Kohrer C, Su D, Russell SP, Krivos K, Castleberry CM, Blum P, Limbach PA, Soll D, RajBhandary UL Proc Natl Acad Sci U S A [details] 20133752 -
Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T Nat Chem Biol [details] 20139989 -
The structural basis for specific decoding of AUA by isoleucine tRNA on the ribosome. Voorhees RM, Mandal D, Neubauer C, Kohrer C, Rajbhandary UL, Ramakrishnan V... Nat Struct Mol Biol [details] 23542153 -

Last modification of this entry: Sept. 22, 2023