Summary

Full name5-hydroxycytidine
IUPAC name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxypyrimidin-2-one
Short nameho5C
MODOMICS code50C
Synonyms
39638-73-8
4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxypyrimidin-2-one
4-Imino-1-pentofuranosyl-1,4-dihydropyrimidine-2,5-diol
5-Hydroxycytidine
AC1L54VN
C9-H13-N3-O6
CCRIS 8241
CHEMBL217770
CID198207
CTK3I9134
Cytidine, 5-hydroxy-
DTXSID80960259
LS-59074
SCHEMBL1138717

Nature of the modified residueNatural
RNAMods codeÇ
Residue unique ID143
Found in RNAYes
Related nucleotides398
Found naturally in RNA typesrRNA

Chemical information

Sum formulaC9H13N3O6
Type of moietynucleoside
Degeneracynot applicable
SMILESNc1nc(=O)[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)cc1O
logP-2.2762
TPSA151.06
Number of atoms18
Number of Hydrogen Bond Acceptors 1 (HBA1)8
Number of Hydrogen Bond Acceptors 2 (HBA2)9
Number of Hydrogen Bond Donors (HBD)5
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/C9H13N3O6/c10-7-3(14)1-12(9(17)11-7)8-6(16)5(15)4(2-13)18-8/h1,4-6,8,13-16H,2H2,(H2,10,11,17)/t4-,5-,6-,8-/m1/s1
InChIKeyMPPUDRFYDKDPBN-UAKXSSHOSA-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
N=C1NC(=O)N(C2OC(CO)C(O)C2O)CC1=O tautomer #0
NC1=NC(=O)N(C2OC(CO)C(O)C2O)CC1=O tautomer #1
N=c1[nH]c(=O)n(C2OC(CO)C(O)C2O)cc1O tautomer #2
Nc1nc(=O)n(C2OC(CO)C(O)C2O)cc1O tautomer #3
N=C1N=C(O)N(C2OC(CO)C(O)C2O)CC1=O tautomer #4
N=c1nc(O)n(C2OC(CO)C(O)C2O)cc1O tautomer #5

Tautomer image Show Image

Predicted CYP Metabolic Sites

CYP3A4 CYP2D6 CYP2C9
ho5C ho5C ho5C

* 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 mass259.0804
Average mass259.216
[M+H]+260.0877
Product ions128
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

TypeSubtype
otherhydroxyl

Reactions producing 5-hydroxycytidine

Name
C:ho5C

Publications

Title Authors Journal Details PubMed Id DOI
Identification of 5-hydroxycytidine at position 2501 concludes characterization of modified nucleotides in E. coli 23S rRNA. Havelund JF, Giessing AM, Hansen T, Rasmussen A, Scott LG, Kirpekar F J Mol Biol [details] 21723290 -
A novel minimum ribozyme with oxidoreduction activity. Yanagawa H, Ogawa Y, Ueno M, Sasaki K, Sato T... Biochemistry [details] 2271669 -

Last modification of this entry: Sept. 29, 2021


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