Thymine (C5H6N2O2): structure, properties and hazards

Names and identifiers

IUPAC name: 5-methyl-1H-pyrimidine-2,4-dione
Synonyms: 5-methyluracil, T, pyrimidine base
+ 34 more
DNA base, 2,4-Dihydroxy-5-methylpyrimidine, Thymin, Thymine anhydrate, 5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione, 2,4(1H,3H)-Pyrimidinedione, 5-methyl-, Thymin (purine base), 5-methyl-1H-pyrimidine-2,4-dione, 5-methyl-2,4(1H,3H)-pyrimidinedione, DTXSID4052342, QR26YLT7LT, NSC14705, CHEBI:17821, NSC-14705, DTXCID4030914, NSC-168663, 5 Methyluracil, RefChem:6308, 200-616-1, 5-methylpyrimidine-2,4(1H,3H)-dione, 5-Methyl Uracil, MFCD00006026, CCRIS 5584, AI3-25479, CHEMBL993, THYMINE-13C1, thymine-d4, 5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE (THYMINE), Thymine-t, Zidovudine EP Impurity C, Thy, Thymine (VAN), (3H)Methylthymidine, 5-methyl-1,3-dihydropyrimidine-2,4-dione
Molecular formula: C₅H₆N₂O₂
Empirical formula: C₅H₆N₂O₂
Molecular weight: 126.11 g/mol
Exact mass: 126.04293
CAS number: 65-71-4
PubChem CID: 1135
Canonical SMILES: CC1=CNC(=O)NC1=O
Isomeric SMILES: CC1=CNC(=O)NC1=O
InChI: InChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)
InChIKey: RWQNBRDOKXIBIV-UHFFFAOYSA-N
Molfile

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

Calculated

Heavy atoms: 9
Rings: 1
Aromatic rings: 1
Fraction sp³ carbons (Fsp3): 0.2
H-bond donors: 2
H-bond acceptors: 2
Rotatable bonds: 0
TPSA (Å²): 65.7 computed here · PubChem 58.2
Formal charge: 0
XLogP3: -0.6 PubChem
Complexity: 195 PubChem
Stereocenters: None
Double-bond geometry: None specified
Point group: Cs of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

C47.62%
H4.80%
N22.21%
O25.37%

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: -0.63 Crippen (Wildman and Crippen 1999)
log S (water solubility): -0.72 ESOL (Delaney 2004), log mol/L
Synthetic accessibility: 2.47 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

Molecular weight ≤ 500: 126.11
log P ≤ 5 (Crippen): -0.63
H-bond donors ≤ 5: 2
H-bond acceptors ≤ 10: 2

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: 7 company reports to ECHA. Source [1].

Harmful or irritant

H319Causes serious eye irritation (42.9% of reports)

Precautionary statements: P264+P265, P280, P305+P351+P338, P337+P317

View all classifications (2)

[1] European Chemicals Agency (ECHA)This chemical does not meet GHS hazard criteria for 57.1% (4 of 7) of all reports.
[1] European Chemicals Agency (ECHA) · 7 reports · WarningH319

Safety data sheets on the supplier’s page: Accel Scientific, Alfa Chemistry, Sinfoo 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]NMRShiftDB · Linked only · 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 Europe · Linked only · via PubChem · retrieved 2026-10-14
[6]MassBank of North America (MoNA) · CC BY 4.0 · via PubChem · retrieved 2026-10-14
[7]NIST Mass Spectrometry Data Center · 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.