Summary

Full name2-lysidine
IUPAC name(2S)-2-amino-6-[[4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-ylidene]amino]hexanoic acid
Short namek2C
MODOMICS code21C
Synonyms
144796-96-3
2-lysylcytidine
4-Amino-2-(N(6)-lysino)-1-ribofuranosylpyrimidine
CHEBI:64328
DTXSID20657499
(E)-N~6~-(4-Amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-ylidene)-L-lysine
J3.522.189A
k(2)C
Lysidine
Lysidine (nucleoside)
lysidine zwitterion
N(6)-[4-imino-1-(beta-D-ribofuranosyl)-1,4-dihydropyrimidin-2-yl]-L-lysine
Q410471

Nature of the modified residueNatural
RNAMods code}
Residue unique ID101
Found in RNAYes
Related nucleotides346
Enzymes TilS (Escherichia coli)
TilS (Geobacillus kaustophilus)
Found in phylogenyEubacteria
Found naturally in RNA typestRNA

Chemical information

Sum formulaC15H25N5O6
Type of moietynucleoside
Degeneracynot applicable
SMILESN[C@H](C(=O)O)CCCCN=c1[n]([C@H]2[C@H](O)[C@H](O)[C@@H](CO)O2)ccc(N)n1
logP-1.1588
TPSA189.44
Number of atoms26
Number of Hydrogen Bond Acceptors 1 (HBA1)10
Number of Hydrogen Bond Acceptors 2 (HBA2)11
Number of Hydrogen Bond Donors (HBD)6
PDB no exac match , link to the most similar ligand AR3
HMDB (Human Metabolome Database) no exac match, link to the most similar ligand HMDB0000089
InChIInChI=1S/C15H25N5O6/c16-8(14(24)25)3-1-2-5-18-15-19-10(17)4-6-20(15)13-12(23)11(22)9(7-21)26-13/h4,6,8-9,11-13,21-23H,1-3,5,7,16H2,(H,24,25)(H2,17,18,19)/t8-,9+,11+,12+,13+/m0/s1
InChIKeyMDWUIKMWKDMPDE-IINAIABHSA-N
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

Tautomers SMILES
NC(C(O)=O)CCCCNc1n(C2C(O)C(O)C(CO)O2)ccc(=N)n1 tautomer #0
N=C(C(O)O)CCCCNc1n(C2C(O)C(O)C(CO)O2)ccc(=N)n1 tautomer #1
NC(C(O)O)=CCCCNc1n(C2C(O)C(O)C(CO)O2)ccc(=N)n1 tautomer #2
NC(C(O)=O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(=N)[nH]1 tautomer #3
N=C(C(O)O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(=N)[nH]1 tautomer #4
NC(C(O)=O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(N)n1 tautomer #5
N=C(C(O)O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(N)n1 tautomer #6
NC(C(O)O)=CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(=N)[nH]1 tautomer #7
NC(C(O)O)=CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(N)n1 tautomer #8
NC(=C(O)O)CCCCNc1n(C2C(O)C(O)C(CO)O2)ccc(=N)n1 tautomer #9
NC(=C(O)O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(=N)[nH]1 tautomer #10
NC(=C(O)O)CCCCN=c1n(C2C(O)C(O)C(CO)O2)ccc(N)n1 tautomer #11

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
k2C k2C k2C

* 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 mass371.1805
Average mass371.389
[M+H]+372.1883
Product ions240
Normalized LC elution time *1,14 (Kellner 2014)
LC elution order/characteristicsbetween G and A (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 grouplysyl

Reactions producing 2-lysidine

Name
C:k2C

Last modification of this entry: Sept. 29, 2021


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