Cytidine (C9H13N3O5): structure, properties and hazards

Names and identifiers

IUPAC name: 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
Synonyms: Cyd, Cytosine riboside, 4-Amino-1-beta-D-ribofuranosyl-2(1H)-pyrimidinone
+ 35 more
1-beta-D-Ribofuranosylcytosine, beta-D-Ribofuranoside, cytosine-1, 1beta-D-Ribofuranosylcytosine, 4-Amino-1beta-D-ribofuranosyl-2(1H)-pyrimidinone, 2(1H)-Pyrimidinone, 4-amino-1-beta-D-ribofuranosyl-, 5CSZ8459RP, CHEBI:17562, DTXSID60891552, 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one, NSC-20258, 4-amino-1-beta-D-ribofuranosylpyrimidin-2(1H)-one, 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2-dihydropyrimidin-2-one, Riboside, Cytosine, Cytosine Ribonucleoside, Ribonucleoside, Cytosine, 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl)pyrimidin-2-one, 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl)-1,2-dihydropyrimidin-2-one, RefChem:388908, DTXCID901030645, 200-610-9, 1beta-Ribofuranosylcytosine, 1-beta-Ribofuranosylcytosine, MFCD00006545, Cytidin, Cytosine, 1-beta-D-ribofuranosyl-, 1beta-2'-Ribofuranosylcytosine, d-, NSC 20258, 2(1H)-Pyrimidinone, 4-amino-1beta-D-ribofuranosyl-, cytosine-1beta-D-Ribofuranoside, 4-amino-1-((2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)pyrimidin-2(1H)-one, 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]pyrimidin-2-one, Cytidine; Cytarabine Impurity E, SMR000058243, 1.beta.-Ribofuranosylcytosine, EINECS 200-610-9
Molecular formula: C₉H₁₃N₃O₅
Empirical formula: C₉H₁₃N₃O₅
Molecular weight: 243.22 g/mol
Exact mass: 243.08552
CAS number: 65-46-3
PubChem CID: 6175
Canonical SMILES: C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
Isomeric SMILES: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
InChI: InChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKey: UHDGCWIWMRVCDJ-XVFCMESISA-N
Molfile

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

Physical properties

TemperaturePressureDensity

Appearance: Cytidine is a white crystalline powder. (NTP, 1992)[1]
Melting point: 215 to 216 °C (419 to 421 °F) (decomposes) (NTP, 1992)[1]
Solubility in water: greater than or equal to 100 mg/mL at 17 °C (63 °F, NTP 1992)[1]
Vapor pressure: Reported, but no value passed the checks.
The value and why
Negligible (NTP, 1992) (could not be read; source [1])

Each value as its source reports it, with the source's number after it (listed under References). Where several sources report a property, the row shows the value most of them agree on, the rule the app uses; open the values to see every one.

Calculated

Heavy atoms: 17
Rings: 2
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0.56
H-bond donors: 4
H-bond acceptors: 7 computed here · PubChem 5
Rotatable bonds: 2
TPSA (Å²): 130.8 computed here · PubChem 129
Formal charge: 0
XLogP3: -2.1 PubChem
Complexity: 383 PubChem
Stereocenters: 4 definedCIP: C3: R · C5: R · C14: R · C16: 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

C44.45%
H5.39%
N17.28%
O32.89%

Isotope pattern

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: -2.56 Crippen (Wildman and Crippen 1999)
log S (water solubility): 0.14 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 3.55 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 243.22
log P ≤ 5 (Crippen): -2.56
H-bond donors ≤ 5: 4
H-bond acceptors ≤ 10: 7

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

Warning

Most widely reported: 6 company reports to ECHA. Source [2].

Harmful or irritant

H315Causes skin irritation (16.7% of reports)
H319Causes serious eye irritation (16.7% of reports)
H335May cause respiratory irritation (16.7% of reports)

Precautionary statements: P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, P501

View all classifications (2)

[2] European Chemicals Agency (ECHA)This chemical does not meet GHS hazard criteria for 83.3% (5 of 6) of all reports.
[2] European Chemicals Agency (ECHA) · 6 reports · WarningH315, H319, H335

First aid

Eyes: First check the victim for contact lenses and remove if present. Flush victim's eyes with water or normal saline solution for 20 to 30 minutes while simultaneously calling a hospital or poison control center. Do not put any ointments, oils, or medication in the victim's eyes without specific instructions from a physician. Immediately transport the victim after flushing eyes to a hospital even if no symptoms (such as redness or irritation) develop. Skin: Immediately flood affected skin with water while removing and isolating all contaminated clothing.[1]

Safety data sheets on the supplier’s page: A2B Chem, MuseChem, TCI (Tokyo Chemical Industry).

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

Spectra

Experimental spectra held by these sources; each link opens the source's own record.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

[1]CAMEO Chemicals · Public domain (NOAA) · via PubChem · retrieved 2026-10-14
[2]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[3]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[4]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[5]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
[6]NIST Mass Spectrometry Data Center · Linked only · via PubChem · retrieved 2026-10-14
[7]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
·Literature on PubChem

Data last updated 2026-10-14.

Similar structures

Tanimoto similarity on Morgan fingerprints (radius 2) with RDKit 2026.09, at least 45%.