Thymidine (C10H14N2O5): structure, properties and hazards

Names and identifiers

IUPAC name: 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione
Synonyms: deoxythymidine, dT, thymine deoxyriboside
+ 35 more
2'-Deoxythymidine, DThyd, Thymidin, Thymine-2-desoxyriboside, 5-Methyl-2'-deoxyuridine, Thyminedeoxyriboside, Deoxyribothymidine, Doxribtimine, dThd, 2'-thymidine, DTXSID5023661, 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methylpyrimidine-2,4-dione, 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione, thymine 2'-deoxyriboside, VC2W18DGKR, 2'-deoxy-5-methyluridine, CHEBI:17748, NSC-21548, DTXCID703661, MT-1621 COMPONENT 2'-DEOXYTHYMIDINE, 1-(2-deoxy-beta-D-erythro-pentofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione, 2' Deoxythymidine, 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl)-5-methylpyrimidine-2,4-dione, 1-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl)-5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione, RefChem:189836, 200-070-4, 5-Methyldeoxyuridine, Beta-Thymidine, 5-Methyldeoxyurindine, Thymine-2-deoxyriboside, 1-((2R,4S,5R)-4-Hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-5-methylpyrimidine-2,4(1H,3H)-dione, Uridine, 2'-deoxy-5-methyl-, Thymine deoxyriboside, MFCD00006537, AI3-52267
Molecular formula: C₁₀H₁₄N₂O₅
Empirical formula: C₁₀H₁₄N₂O₅
Molecular weight: 242.23 g/mol
Exact mass: 242.09027
CAS number: 50-89-5
PubChem CID: 5789
Canonical SMILES: CC1=CN(C(=O)NC1=O)C2CC(C(O2)CO)O
Isomeric SMILES: CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
InChI: InChI=1S/C10H14N2O5/c1-5-3-12(10(16)11-9(5)15)8-2-6(14)7(4-13)17-8/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
InChIKey: IQFYYKKMVGJFEH-XLPZGREQSA-N
Molfile

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

Calculated

Heavy atoms: 17
Rings: 2
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0.6
H-bond donors: 3
H-bond acceptors: 5
Rotatable bonds: 2
TPSA (Å²): 104.5 computed here · PubChem 99.1
Formal charge: 0
XLogP3: -1.2 PubChem
Complexity: 381 PubChem
Stereocenters: 3 definedCIP: C5: R · C7: S · C9: R
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

C49.58%
H5.83%
N11.56%
O33.02%

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: -1.51 Crippen (Wildman and Crippen 1999)
log S (water solubility): -0.52 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 3.38 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 242.23
log P ≤ 5 (Crippen): -1.51
H-bond donors ≤ 5: 3
H-bond acceptors ≤ 10: 5

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

This chemical does not meet GHS hazard criteria for 97.6% (121 of 124) of all reports.[1]

Safety data sheets on the supplier’s page: Fluorochem, Sigma-Aldrich, NewCan Biotech.

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]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
[2]Human Metabolome Database (HMDB) · Linked only · via PubChem · retrieved 2026-10-14
[3]SpectraBase · Linked only · via PubChem · retrieved 2026-10-14
[4]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
[5]MassBank Europe · Linked only · via PubChem · retrieved 2026-10-14
[6]NCI Investigational Drugs · 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%.