After getting help from EBI support I got a db of ligand binding sites from PDBeMotif database working, quite up-to-date and local.
I am using it for some time already, and it seems to be cool. It basically lists all bonds to hetatms from PDB, together with distance info, and with annotations on interaction type.
I wrote some quick-and-dirty Python code to download and use this db.
pip install http://modorama.biocomputing.it/beta_static/src/pdbemotif-0.1.0.tar.gz
It should install
pdbemotif Python module, and two scripts should go to your python bin:
They download data on bonds with protein and hetatms. You can use like this:
python -u path_to_bin/download_all_lig_sites.py /data1/outdir/
python -u path_to_bin/download_selected_lig_sites.py some_pdbcodes.txt /data1/tmp/outdir/
some_pdbcodes.txt file lists pdbcodes, one per each line.
Downloading all "sites" takes 3 days. You will get a list of xml files, one per each pdbcode.
Then you can do:
from pdbemotif import BoundMoleculeSite
site_file = open('/data/db/PDBeMotif/3mht.txt')
mol_site = BoundMoleculeSite(site_file.read())