Modomics - A Database of RNA Modifications

hn6A
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 nameN6-hydroxynorvalylcarbamoyladenosine
Short namehn6A
MODOMICS code new2000000063A
MODOMICS code63A
Nature of the modified residueNatural
RNAMods code√
Residue unique ID19
Found in RNAYes
Related nucleotides437

Chemical information

Sum formulaC16H22N6O8
Type of moietynucleoside
Degeneracynot applicable
SMILESCCC(O)C(NC(Nc1ncnc2c1nc[n]2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O)=O)C(O)=O
logP-1.7527
TPSA212.18
Number of atoms30
Number of Hydrogen Bond Acceptors 1 (HBA1)13
Number of Hydrogen Bond Acceptors 2 (HBA2)14
Number of Hydrogen Bond Donors (HBD)7
PDB no exac match , link to the most similar ligand AET
HMDB (Human Metabolome Database) no exact match, link to the most similar ligand None
InChIInChI=1S/C16H22N6O8/c1-2-6(24)8(15(27)28)20-16(29)21-12-9-13(18-4-17-12)22(5-19-9)14-11(26)10(25)7(3-23)30-14/h4-8,10-11,14,23-26H,2-3H2,1H3,(H,27,28)(H2,17,18,20,21,29)/t6?,7-,8?,10-,11-,14-/m1/s1
InChIKeyCKYYHBNGEDJKKW-DGTGAXRRSA-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
CCC(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(=O)O tautomer #0
CCC(=O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #1
CCC(O)C(=NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #2
CCC(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(=O)O tautomer #3
CCC(=O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #4
CCC(O)C(=NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #5
CC=C(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #6
CCC(O)=C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #7
CCC(O)C(NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)C(=O)O tautomer #8
CCC(=O)C(NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #9
CCC(O)C(=NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #10
CC=C(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #11
CCC(O)=C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #12
CCC(O)C(NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(=O)O tautomer #13
CCC(=O)C(NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #14
CCC(O)C(=NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #15
CCC(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)=C(O)O tautomer #16
CCC(O)C(N=C(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #17
CC=C(O)C(NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #18
CCC(O)=C(NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #19
CCC(O)C(NC(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)=O)=C(O)O tautomer #20
CCC(O)C(N=C(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #21
CCC(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #22
CCC(=O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #23
CCC(O)C(=NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #24
CC=C(O)C(NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #25
CCC(O)=C(NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #26
CCC(O)C(NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)C(=O)O tautomer #27
CCC(=O)C(NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #28
CCC(O)C(=NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #29
CCC(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #30
CCC(=O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #31
CCC(O)C(=NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #32
CCC(O)C(NC(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)=O)=C(O)O tautomer #33
CCC(O)C(N=C(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #34
CC=C(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #35
CCC(O)=C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #36
CCC(O)C(NC(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)=O)=C(O)O tautomer #37
CCC(O)C(N=C(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #38
CC=C(O)C(NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #39
CCC(O)=C(NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)C(O)O tautomer #40
CC=C(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #41
CCC(O)=C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)C(O)O tautomer #42
CCC(O)C(N=C(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #43
CCC(O)C(N=C(Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #44
CCC(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #45
CCC(O)C(NC(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)=O)=C(O)O tautomer #46
CCC(O)C(N=C(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)O)C(=O)O tautomer #47
CCC(O)C(NC(=Nc1ncnc2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #48
CCC(O)C(N=C(N=c1nc[nH]c2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #49
CCC(O)C(N=C(N=c1[nH]cnc2c1ncn2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #50
CCC(O)C(N=C(N=C1N=CN=C2C1N=CN2C3OC(CO)C(O)C3O)O)=C(O)O tautomer #51
Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
hn6A hn6A hn6A

* 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 mass426.1499
Average mass426.381
[M+H]+427.1577
Product ions295
Normalized LC elution time *1,93 (Kellner 2014)
LC elution order/characteristicsbetween 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 -

Chemical groups contained

TypeSubtype
aminoacyl groupnorvalyl
othercarbamoyl
otherhydroxyl

Reactions producing N6-hydroxynorvalylcarbamoyladenosine

Name
A:hn6A

Reactions starting from N6-hydroxynorvalylcarbamoyladenosine

Name
hn6A:ms2hn6A

Publications

Title Authors Journal Details PubMed Id DOI
Structure determination of two new amino acid-containing derivatives of adenosine from tRNA of thermophilic bacteria and archaea. Reddy DM, Crain PF, Edmonds CG, Gupta R, Hashizume T, Stetter KO, Widdel F, McCloskey JA... Nucleic Acids Res [details] 1280806 -

Last modification of this entry: Sept. 22, 2023