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Deoxycytidine

Athanor · official

C9H13N3O4 · 227.22 g/mol

IUPAC name: 4-amino-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one

Also called dC

Nucleic acid partsDNA
Open in Athanor
The structure of Deoxycytidine
Drawn from its SMILES with RDKit

Names and identifiers

IUPAC name
4-amino-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Synonyms
dC, 2'-DEOXY-ALPHA-CYTIDINE, 4-amino-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one
+ 10 more

4-Amino-1-((2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one, 2'-Deoxy-a-cytidine, 2'-DEOXY-L-CYTIDINE, 4-amino-1-[(2S,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one, ranosyl)-2(1H )-pyrimidinone, SCHEMBL41984993, EBC-48112, 4-Amino-1-(2-deoxy-alpha-D-erythro -pentofu, EN300-20600017, 2(1H)-Pyrimidinone, 4-amino-1-(2-deoxy-alpha-D-erythro-pentofuranosyl)-

Molecular formula
C9H13N3O4
Empirical formula
C9H13N3O4
Molecular weight
227.22 g/mol
Exact mass
227.09061
CAS number
951-77-9
PubChem CID
1223201
Canonical SMILES
C1C(C(OC1N2C=CC(=NC2=O)N)CO)O
Isomeric SMILES
C1[C@@H]([C@H](O[C@@H]1N2C=CC(=NC2=O)N)CO)O
InChI
InChI=1S/C9H13N3O4/c10-7-1-2-12(9(15)11-7)8-3-5(14)6(4-13)16-8/h1-2,5-6,8,13-14H,3-4H2,(H2,10,11,15)/t5-,6+,8-/m0/s1
InChIKey
CKTSBUTUHBMZGZ-BBVRLYRLSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms
16
Rings
2
Aromatic rings
1
Fraction sp³ carbons (Fsp3)
0.56
H-bond donors
3
H-bond acceptors
6 computed here · PubChem 4
Rotatable bonds
2
TPSA (Ų)
110.6 computed here · PubChem 108
Formal charge
0
XLogP3
-1.8 PubChem
Complexity
355 PubChem
Stereocenters
3 definedCIP: C3: R · C5: R · C15: S
Double-bond geometry
None specified
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C47.57%
  • H5.77%
  • N18.49%
  • O28.16%

Isotope pattern

100%227.09111%228.0931.4%229.095230.098

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
-1.53 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-0.43 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
3.51 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 227.22
  • log P ≤ 5 (Crippen): -1.53
  • H-bond donors ≤ 5: 3
  • H-bond acceptors ≤ 10: 6

Passes all four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

No GHS hazard classification was found in the sources.

Safety data sheets on the supplier’s page: DempoChem, Finetech Industry Limited, Angene Chemical.

Always read the supplier’s safety data sheet before working with it.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  2. ·Literature on PubChem

Data last updated 2026-10-14.