I do not know to have availabe database for small molecules in *PDB format. Only for ptoteins as you most probably also know (http://www.rcsb.org/pdb/home/home.do). But *.pdb format give you info for the structural coordinates and if you have *.mol (or mol2) files they can be easy converted to *pdb ones. Same is valid for *.pdb-to-mol (mol2) conversion.
I do not know to have availabe database for small molecules in *PDB format. Only for ptoteins as you most probably also know (http://www.rcsb.org/pdb/home/home.do). But *.pdb format give you info for the structural coordinates and if you have *.mol (or mol2) files they can be easy converted to *pdb ones. Same is valid for *.pdb-to-mol (mol2) conversion.
For drugs, Yau may use DrugBank (http://www.drugbank.ca/downloads#structures). Here you will get structures in SDF format and you can use babel or other software or webserver (http://www.webqc.org/molecularformatsconverter.php) to convert them in PDB format.
the above gives you world drugs (per DrugBank approved) as 3D models in ready-to-dock formats near physiological pH. If you prefer just FDA approved drugs, and just one model at pH 7, use:
if you know the structure you can draw it in chem ultra 12.0 software. copy it and paste in chemdraw 3D software.after that in chemdraw 3D software go through the steps
calculation>MM2>Minimize energy and molecular dynamics.
finally save it as .pdb file.both software are freely available.for any query i m happy to help you