How To Confirm The Presence Of 3D Structure Of A Small Molecule?

Question

[Lavanya]

how to confirm the presence of a 3d structure of a small molecule? is there any database to confirm or is there any method to confirm?

Answer 1

[Pals]

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.

Answer 2

[Woa]

CCDC, The Cambridge crystallographic data centre contains many small molecule structures possibly more than PDB

Answer 3

[Chris]

Not sure what you mean by 'presence'. Take a look at pdb perhaps, which contains protein structures having small molecules bound.

Answer 4

[Egon Willighagen]

There is no public index that spans multiple databases. But there are some open resources for experimental crystal structures of small molecules:

• PDBe
• CrystalEye
• Crystallography Open Database