Question: How To Confirm The Presence Of 3D Structure Of A Small Molecule?
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Of course you can have a look on PDB. Otherwise there are also dozens of databases dedicated for small molecules: for example PubChem http://pubchem.ncbi.nlm.nih.gov/, or the one maintained by EBI http://www.ebi.ac.uk/Databases/smallmolecules.html. Search your small molecule by its name and hopefully you will get the structure if it has been deposited.
There is no public index that spans multiple databases. But there are some open resources for experimental crystal structures of small molecules: