trans-4-Hydroxy-D-proline

A summary of the most common chemical descriptors (InChI Key and SMILES codes) for trans-4-Hydroxy-D-proline are summarized together with 3D and 2D structures and relevant physico-chemical properties.

What is the trans-4-Hydroxy-D-proline?

The molecule trans-4-Hydroxy-D-proline presents a molecular formula of C₅H₉NO₃ and its IUPAC name is (2R,4S)-4-hydroxypyrrolidine-2-carboxylic acid.

Proline is an amino acid that is commonly found in proteins. It is a non-essential amino acid, which means that the body can synthesize it. Proline is a hydrophobic amino acid, which means that it does not dissolve in water. Trans-4-hydroxy-D-proline (4-OH-D-Pro) is a proline derivative that belongs in some proteins. 4-OH-D-Pro is a hydrophilic amino acid, which means that it dissolves in water. 4-OH-D-Pro is also a zwitterion, which means that it has both a positive and a negative charge. 4-OH-D-Pro is an important amino acid for the structure and function of proteins..

4-OH-D-Pro belongs in proteins that are involved in cell signaling, cell adhesion, and cell motility. 4-OH-D-Pro is also found in proteins that are involved in the immune response. 4-OH-D-Pro is a substrate for the enzyme proline dehydrogenase. Proline dehydrogenase catalyzes the conversion of 4-OH-D-Pro to 4-oxo-D-proline. 4-oxo-D-proline is an intermediate in the urea cycle. The urea cycle is a process that removes ammonia from the body. Ammonia is a toxic waste product that is produced when proteins are broken down. The urea cycle converts ammonia to urea, which is then excreted in the urine..

4-OH-D-Pro is an important amino acid for the structure and function of proteins. Proteins that contain 4-OH-D-Pro are involved in cell signaling, cell adhesion, cell motility, and the immune response. 4-OH-D-Pro is also a substrate for the enzyme proline dehydrogenase. Proline dehydrogenase catalyzes the conversion of 4-OH-D-Pro to 4-oxo-D-proline. 4-oxo-D-proline is an intermediate in the urea cycle. The urea cycle is a process that removes ammonia from the body. Ammonia is a toxic waste product that is produced when proteins are broken down. The urea cycle converts ammonia to urea, which is then excreted in the urine..

3D structure

Cartesian coordinates

Geometry of trans-4-Hydroxy-D-proline in x, y and z coordinates (Å units) to copy/paste elsewhere. Generated with Open Babel software.

2D drawing

Molecule descriptors

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.

Reference codes for other databases

• CAS number (Chemical Abstracts Service Registry Number) is a unique identifier is assigned to every chemical compound indexed in the CAS database.
• Beilstein: The Beilstein database is a comprehensive source of information on organic chemistry, including information on chemical structures, properties, and reactions. The Beilstein database assigns unique identifiers which can be used to identify compounds in scientific literature and other sources.
• ChEBI (Chemical Entities of Biological Interest): ChEBI is a database of small chemical molecules that are of interest in the field of biology.
• PubChem CID (Compound Identifier): PubChem is a database of chemical compounds that is maintained by the National Institutes of Health (NIH).
• RTECS number (Registry of Toxic Effects of Chemical Substances): The RTECS is a database of information on the toxic effects of chemicals, including information on their structures and properties.
• ChEMBL (Compound Bioactivity Data): ChEMBL is a database of bioactivity data for small molecules, including information on their properties and structures.
• CompTox Dashboard (Environmental Protection Agency): The CompTox Dashboard is a database of information on the toxicology and environmental effects of chemicals.

Physico-Chemical properties

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

The n-octanol/water partition coeficient (K_ow) data is applied in toxicology and drug research. K_ow 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(K_ow) (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 Ų are required. Thus, molecules with a polar surface area greater than 140 Ų tend to be poorly permeable to cell membranes.