Summary
| Full name | 5-hydroxycytidine |
| IUPAC name | 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-hydroxypyrimidin-2-one |
| Short name | ho5C |
| MODOMICS code new | 2000000050C |
| MODOMICS code | 50C |
| 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 residue | Natural |
| RNAMods code | Ç |
| Residue unique ID | 143 |
| Found in RNA | Yes |
| Related nucleotides | 398 |
| Found naturally in RNA types | rRNA |
Chemical information
| Sum formula | C9H13N3O6 |
| Type of moiety | nucleoside |
| Degeneracy | not applicable |
| SMILES | Nc1nc(=O)[n]([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)cc1O |
| logP | -2.2762 |
| TPSA | 151.06 |
| Number of atoms | 18 |
| 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 exact match, link to the most similar ligand | None |
| InChI | InChI=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 |
| InChIKey | MPPUDRFYDKDPBN-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 |
|---|---|---|
|
|
|
* 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 mass | 259.0804 |
| Average mass | 259.216 |
| [M+H]+ | 260.0877 |
| Product ions | 128 |
| 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
| Type | Subtype |
|---|---|
| other | hydroxyl |
Reactions producing 5-hydroxycytidine
| Name |
|---|
| C:ho5C |
Publications
| Title | Authors | Journal | Details | ||
|---|---|---|---|---|---|
| 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. 22, 2023