On www.pdb.org, there are many structures with both proteins and corresponding ligands (small molecules) present. Usually, those ligands are assigned different three-letter codes (similar to other residues).
I wonder who assigns these three letter codes for ligands, and more importantly, how to assign a three-letter code for a generic organic small molecule.
Is there a standard/recommended means to generate three-letter codes for small molecules?
Thanks for any comments,
Yun
If your ligand is not already in the PDB, the staff at the PDB will assign a new 3-letter code for your molecule upon deposition. Regarding the rationale behind it, I would say it's generated randomly, like the assignment of macromolecular PDB codes.
The three-letter codes are generally picked by the crystallographer during refinement. In the past, I have picked codes that closely resemble the common chemical name of the compound, or are memorable enough (for me!) AND have not been used previously for any structure deposited in the PDB.
So, in essence, it is pretty random!
The above answers are right. The codes are assigned by PDB annotators during annotation. If your ligand matches a molecule already present, we will reassign it to that code. If it's new, we'll give it a new code.
Some of the older ligands have meaningful three letter codes (eg ATP) but there are now far too many for that to be possible. The most common three letter codes for small molecules in the deposited files are LIG, DRG or INH (ligand, drug, inhibitor)
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