Mr. Zidan,
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.
You can also use open babel software to conert different file format to any other format.
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.
For synthetic molecule, you used DrugBank, Zinc Database and PUBCHEM Database. and for conversion used Openbable Software.
http://zinc15.docking.org/protomers/subsets/usual/having/substance/subsets/world.sdf?count=all
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:
http://zinc15.docking.org/protomers/subsets/ref/having/substance/subsets/fda.sdf?count=all
Good luck
We don't actually offer PDB (buy why would you want that?)
You can use openbabel to convert from SDF (or mol2) to PDB.
Dear Ahmad
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
Hi , In addition to above if you couldn't find the pdb structure you can download a complex pdb file (complex of your molecule and a protein for example) and delete protein structure in the file.
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