A summary of the most common chemical descriptors (InChI Key and SMILES codes) for Thymine are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the Thymine?

The molecule Thymine presents a molecular formula of C5H6N2O2 and its IUPAC name is 5-methyl-1H-pyrimidine-2,4-dione.

Thymine is a nitrogenous base that is one of the four building blocks of DNA (deoxyribonucleic acid). It is a pyrimidine base, meaning that it is composed of a six-membered ring with two nitrogen atoms at positions 1 and 3. Along with adenine, guanine, and cytosine, thymine plays a vital role in the structure and function of DNA..

In DNA, thymine is paired with adenine through a process called hydrogen bonding. This pairing helps to stabilize the double helix structure of DNA, which is essential for the transmission of genetic information from one generation to the next..

Thymine is synthesized in the body through the de novo pathway, which involves the conversion of uridine monophosphate (UMP) into thymine monophosphate (TMP). It can also be obtained through the diet, as it belongs in some foods, such as eggs and dairy products..

Thymine is important for maintaining the integrity of the genome and is involved in a number of biological processes, including DNA repair and DNA methylation. It has also been the subject of research for its potential role in cancer and other diseases..


From all the above, this molecule is a nitrogenous base that is essential for the structure and function of DNA. It is involved in a number of important biological processes and has been the subject of extensive research for its potential role in diseases such as cancer..

3D structure

Cartesian coordinates

Geometry of Thymine in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing


Thymine RWQNBRDOKXIBIV-UHFFFAOYSA-N chemical compound 2D structure molecule svg


Molecule descriptors

IUPAC name5-methyl-1H-pyrimidine-2,4-dione
InChI codeInChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)

Other names (synonyms)

IUPAC nomenclature provides a standardized method for naming chemical compounds. Although this system is widely used in chemistry, many chemical compounds have also other names commonly used in different contexts. These synonyms can come from a variety of sources and are used for a variety of purposes.

One common source of synonyms for chemical compounds is the common or trivial names, assigned on the basis of appearance, properties, or origin of the molecule.

Another source of synonyms are historical or obsolete names employed in the past, however replaced nowadays by more modern or standardized names.

In addition to common and historical names, chemical compounds may also have synonyms that are specific to a particular field or industry.

  • (3H)Methylthymidine
  • 006T026
  • 036B9F1D-9B61-4CED-967C-BF1DA180E5C2
  • 123430-67-1
  • 153445-43-3
  • 2,3H)-Pyrimidinedione, 5-methyl-
  • 2,4(1H,3H)-Pyrimidinedione, 5-methyl-
  • 2,4(1H,3H)-Pyrimidinedione, 5-methyl- (9CI)
  • 2,4(1H,3H)-Pyrimidinedione, 5-methyl-, labeled with tritium
  • 2,4-Dihydroxy-5-methylpyrimidine
  • 2.6-Dioxy-5-methyl-pyrimidin
  • 2792-47-4
  • 3059-73-2
  • 4(1H)-Pyrimidinone, 2-hydroxy-5-methyl- (9CI)
  • 4(3H)-Pyrimidinone, 2-hydroxy-5-methyl- (9CI)
  • 4-Hydroxy-5-methylpyrimidin-2(1H)-one
  • 5-Methyl Uracil
  • 5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione
  • 5-Methyl-2,4-dihydroxypyrimidine
  • 5-Methyl-2,4-dioxypyrimidine
  • 5-Methylpyrimidine-2,4-dione
  • 5-methy uracil(Thymine)
  • 5-methyl-1H-pyrimidine-2,4-dione
  • 5-methyl-2,4(1H,3H)-pyrimidinedione
  • 5-methyl-uracil
  • 5-methylpyrimidine-2,4(1H,3H)-dione
  • 5-methylpyrimidine-2,4-diol
  • 5-methyluracil
  • 65-71-4
  • A835203
  • AC-7756
  • AI3-25479
  • AM81332
  • BCP22973
  • BDBM50134397
  • C00178
  • CCG-266101
  • CCRIS 5584
  • CID 5274265
  • CS-W011166
  • DB-016098
  • DB03462
  • DSSTox_CID_30914
  • DSSTox_GSID_52342
  • Epitope ID:167476
  • F0001-1753
  • FT-0602550
  • FT-0675207
  • FT-0771534
  • GTPL4581
  • HY-W010450
  • MFCD00006026
  • Methyl-3H thymidine
  • NCGC00357169-01
  • NSC 14705
  • NSC-14705
  • NSC-168663
  • NSC14705
  • Q171973
  • QR26YLT7LT
  • SB57778
  • SR-01000945223
  • SR-01000945223-1
  • STL280241
  • STL477641
  • SY014896
  • T-3845
  • T0234
  • Thy
  • Thymin
  • Thymin (purine base)
  • Thymine
  • Thymine (8CI)
  • Thymine anhydrate
  • Thymine,(S)
  • Thymine-t
  • Thymine; USP Zidovudine Related Compound C; 5-Methyluracil; 5-Methylpyrimidine-2,4(1H,3H)-dione; 4-Hydroxy-5-methylyrimidin-2(1H)-one
  • Zidovudine EP Impurity C
  • Zidovudine Related Compound C
  • s9382
  • thymine

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC157062
  • CAS-65-71-4
  • AKOS000120923
  • AKOS002337369
  • DTXSID4052342
  • CHEMBL993
  • CHEBI:17821
  • Tox21_303929
  • EINECS 200-616-1
  • SCHEMBL5235
  • SCHEMBL15496760
  • SCHEMBL16356870

Physico-Chemical properties

IUPAC name5-methyl-1H-pyrimidine-2,4-dione
Molecular formulaC5H6N2O2
Molecular weight126.11
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity32.6
Topological polar surface area65.7

LogP and topological polar surface area (TPSA) values were estimated using Open Babel software.

The n-octanol/water partition coeficient (Kow) data is applied in toxicology and drug research. Kow values are used, to guess the environmental fate of persistent organic pollutants. High partition coefficients values, tend to accumulate in the fatty tissue of organisms. Molecules with a log(Kow) (or LogP) greater than 5 are considered to bioaccumulate.

TPSA values are the sum of the surface area over all polar atoms or molecules, mainly oxygen and nitrogen, also including hydrogen atoms.

In medicinal chemistry, TPSA is used to assess the ability of a drug to permeabilise cells.

For molecules to penetrate the blood-brain barrier (and act on receptors in the central nervous system), TPSA values below 90 Å2 are required. Thus, molecules with a polar surface area greater than 140 Å2 tend to be poorly permeable to cell membranes.