Modomics - A Database of RNA Modifications

ct6A
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 namecyclic N6-threonylcarbamoyladenosine
Short namect6A
MODOMICS code new2000000069A
MODOMICS code69A
Nature of the modified residueNatural
RNAMods codee
Residue unique ID175
Found in RNAYes
Related nucleotides413
Enzymes TcdA (Escherichia coli)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC15H18N6O7
Type of moietynucleoside
Degeneracynot applicable
SMILESCC(O)C1NC(=Nc2ncnc3c2nc[n]3[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)OC1=O
logP-2.3501
TPSA184.44
Number of atoms28
Number of Hydrogen Bond Acceptors 1 (HBA1)12
Number of Hydrogen Bond Acceptors 2 (HBA2)13
Number of Hydrogen Bond Donors (HBD)5
PDB no exac match , link to the most similar ligand 37H
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C15H18N6O7/c1-5(23)7-14(26)28-15(19-7)20-11-8-12(17-3-16-11)21(4-18-8)13-10(25)9(24)6(2-22)27-13/h3-7,9-10,13,22-25H,2H2,1H3,(H,16,17,19,20)/t5?,6-,7?,9-,10-,13-/m1/s1
InChIKeyNIMLOKNRDJCYPO-HZPYULPISA-N
Search the molecule in external databases ChEMBL  ChemAgora  ChEBI  PubChem Compound Database  Ligand Expo  ChemSpider  WIPO 

* 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

Tautomers SMILES
CC(O)c1nc(Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)oc1O tautomer #0
CC(O)c1nc(Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)oc1O tautomer #1
CC(O)C1N=C(Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1=O tautomer #2
CC(=O)C1NC(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1O tautomer #3
CC(O)C1=NC(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1O tautomer #4
CC(O)C1NC(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1=O tautomer #5
CC(O)C1N=C(Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1=O tautomer #6
CC(O)c1nc(N=c2nc[nH]c3c2ncn3C4OC(CO)C(O)C4O)oc1O tautomer #7
CC(O)c1nc(N=c2[nH]cnc3c2ncn3C4OC(CO)C(O)C4O)oc1O tautomer #8
CC(O)C1N=C(N=c2nc[nH]c3c2ncn3C4OC(CO)C(O)C4O)OC1=O tautomer #9
C=C(O)C1NC(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1O tautomer #10
CC(O)c1[nH]c(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)oc1O tautomer #11
CC(O)=C1NC(=Nc2ncnc3c2ncn3C4OC(CO)C(O)C4O)OC1O tautomer #12
CC(O)C1N=C(N=c2[nH]cnc3c2ncn3C4OC(CO)C(O)C4O)OC1=O tautomer #13
CC(O)c1nc(N=C2N=CN=C3C2N=CN3C4OC(CO)C(O)C4O)oc1O tautomer #14
CC(O)C1N=C(N=C2N=CN=C3C2N=CN3C4OC(CO)C(O)C4O)OC1=O tautomer #15
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ct6A ct6A ct6A

* 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 mass394.1237
Average mass394.339
[M+H]+395.1315
Product ions263
Normalized LC elution time *1,28 (Kellner 2014); 1,47 (Kellner 2014); 1,83 (Kellner 2014)
LC elution order/characteristicsbetween G and A (Kellner 2014); between A and m6A (Kellner 2014);

* normalized to guanosine (G), measured with a RP C-18 column with acetonitrile/ammonium acetate as mobile phase.


LC-MS Publications

Title Authors Journal Details PubMed Id DOI
Profiling of RNA modifications by multiplexed stable isotope labelling. Kellner S, Neumann J, Rosenkranz D, Lebedeva S, Ketting RF, Zischler H, Schneider D, Helm M. Chem Commun (Camb). [details] 24567952 -

Reactions producing cyclic N6-threonylcarbamoyladenosine

Name
t6A:ct6A

Reactions starting from cyclic N6-threonylcarbamoyladenosine

Name
ct6A:t6A

Last modification of this entry: Sept. 22, 2023