Hello!
I have a question concerning PharmaDB binding sites database. Is it only based on sc-PDB database or were there more 3D structures added during the curating process? And if so, is there any way I can get the full list of all Pharma-DB binding sites? Also, are PharmaDB and sc-PDB non-redundant databases or not?
Here's my issue: according to the 2014 release article of sc-PDB ( https://academic.oup.com/nar/article/43/D1/D399/2439494?login=true ), the database is "non-redundant" and there isn't twice the same protein-ligand complex is the database. However, I looked at the screening results of my Ligand Profiler protocol (done on PharmaDB), and I found 4 different PDB structure entries with the same protein/ligand complex (PDE4D in complex with Rolipram): 1tbb, 1q9m, 3g4k, 1oyn. I found them again in the full sc-PDB 2017 release I have on my computer. So my question is: is PharmaDB really a non-redundant database, as said in the article, or not? And if it is and there is supposed to be some filtering for non-redundancy, how did these structures get through?

Thank you in advance!