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In its usual sense, ligand denotes a small molecule bound non-covalently to a macromolecule. The binding is typically reversible. Examples: Receptors bind hormone and cytokine ligands, and enzymes bind substrate or inhibitor ligands. Avidin binds the ligand biotin.

The green links that Proteopedia places beneath molecules under the category Ligands are based on a somewhat different definition, as explained below.

In macromolecular structure, ligand has a specialized and somewhat different meaning derived from the way in which the PDB file format is structured. All atoms in PDB files are classified into two groups: atoms in standard residues of protein or nucleic acid chains, identified with the ATOM record type, and all other atoms, which are identified with the HETATM record type.

Many visualization and modeling programs further divide hetero atoms into solvent and non-solvent atoms. Solvent includes water and common anions such as sulfate and phosphate ions. These programs (e.g. RasMol, Chime, and Jmol) often define ligand to include all non-solvent hetero atoms. In these programs, selecting and displaying ligand will display, for example, all carbohydrate, whether or not covalently linked to a protein, in addition to moieties ordinarily considered to be ligand, such as metal ions and small organic compounds other than standard residues.

Some things that would ordinarily be considered to be ligands will fail to be included when ligand is selected and displayed in Jmol (or RasMol or Chime). These include single amino acids or nucleotides, peptide ligands, DNA or RNA bound to a protein as ligands. FirstGlance in Jmol uses special code to display single standard residues or non-standard residues as ligand, which avoid them being invisible in a backbone-only display such as a secondary structure schematic cartoon.

At RCSB.Org, using the Advanced Search and query type Chemical ID, you can find all entries in the database that contain a particular chemical component. For example, in December, 2019, five entries contain PYL (explained in Non-Standard Residues).

A complete list of all compounds in the PDB is available, including hydrogens, 3D structures, and bond orders, in the Chemical Components Dictionary of the Worldwide Protein Data Bank. This includes all Standard Residues as well as Non-Standard Residues, carbohydrate adducts, Ligands and Hetero Groups. It is updated weekly for newly released entries.

The PDBbind Database provides a comprehensive collection of annotations of experimentally measured binding affinities, such as Kd, Ki, or IC50, for all biomolecular-ligand complexes deposited in the Protein Data Bank (PDB).

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Eric Martz, Wayne Decatur, Jaime Prilusky, Eran Hodis

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