Secnidazole, (R)-

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

What is the Secnidazole, (R)-?

The molecule Secnidazole, (R)- presents a molecular formula of C7H11N3O3 and its IUPAC name is (2R)-1-(2-methyl-5-nitroimidazol-1-yl)propan-2-ol.

Secnidazole, (R)- is a molecule that belongs to the class of imidazoles. It is a white to off-white crystalline powder that is insoluble in water. The (R)-isomer of secnidazole is a potent and selective inhibitor of histone deacetylase (HDAC) enzymes. Histone deacetylases are enzymes that remove acetyl groups from histones, which are the proteins that make up chromatin. Chromatin is the material that makes up the chromosomes in cells..

The (R)-isomer of secnidazole has been shown to inhibit the growth of cancer cells in vitro and in vivo. In a mouse model of human breast cancer, the (R)-isomer of secnidazole inhibited the growth of the tumors and increased the survival of the animals. The (R)-isomer of secnidazole has also been shown to inhibit the growth of colon cancer cells in vitro and in vivo. In a mouse model of human colon cancer, the (R)-isomer of secnidazole inhibited the growth of the tumors and increased the survival of the animals..

The (R)-isomer of secnidazole is being investigated as a potential treatment for cancer..

3D structure

Cartesian coordinates

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

2D drawing


Secnidazole, (R)- KPQZUUQMTUIKBP-RXMQYKEDSA-N chemical compound 2D structure molecule svg
Secnidazole, (R)-


Molecule descriptors

IUPAC name(2R)-1-(2-methyl-5-nitroimidazol-1-yl)propan-2-ol
InChI codeInChI=1S/C7H11N3O3/c1-5(11)4-9-6(2)8-3-7(9)10(12)13/h3,5,11H,4H2,1-2H3/t5-/m1/s1

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.

  • (2R)-1-(2-methyl-5-nitroimidazol-1-yl)propan-2-ol
  • (R)-secnidazole
  • (alphaR)-alpha,2-Dimethyl-5-nitro-1H-imidazole-1-ethanol
  • 1H-Imidazole-1-ethanol, alpha,2-dimethyl-5-nitro-, (alphaR)
  • 618911-61-8
  • 7551F316CJ
  • Q27896193
  • Secnidazole, (-)-
  • Secnidazole, (R)-

Reference codes for other databases

There exist several different chemical codes commonly used in orded to identify molecules:
  • ZINC711
  • UNII-7551F316CJ
  • SCHEMBL363925

Physico-Chemical properties

IUPAC name(2R)-1-(2-methyl-5-nitroimidazol-1-yl)propan-2-ol
Molecular formulaC7H11N3O3
Molecular weight185.181
Melting point (ºC)
Boiling point (ºC)
Density (g/cm3)
Molar refractivity48.05
Topological polar surface area83.9

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.