Pdb File Of Drug

Question

[Surendrs]

hello friends

can anyone help to tell how to get pdb file of drug molecule?

surendra

Answer 1

[Egon Willighagen]

You can download 3D models for drugs from many databases, including PubChem, ChemSpider, and DrugBank. You can then use OpenBabel to convert those models into PDB files.

Answer 2

[Michael Kuhn]

What do you mean? Drugs as they have been found to bind to proteins? In this case, the SuperLigand database might help you (e.g. ibuprofen). There's also the subscription-based Cambridge Structural Database. Lastly, a Google search finds DrugPort (e.g. ibuprofen).

Answer 3

[Nir London]

If I understand correctly, surendra, you managed to convert to PDB but failed to view it in Discovery Studio? Perhaps try to convert it to a mol2 file (if it's not already the native format) and that would go through better.

Answer 4

[Surendra]

thanks Egon W and M Kuhn for giving answer,, @ Egon as you told me download 3d model and then convert into pdb files,,,it does work,,i got coordinates of my drug in openbabel software ,,, but i got stuck when these pdb files converting into pdb viewer.my question is how do we convert these pdb files coordinates into pdb viewer? i have discovery studio software for viewing pdb files.i am not able to convert these file coordinates into pdb form for further use.

[Egon Willighagen]

Please explain what you mean with converting a PDB file into a PDB viewer... and I do not get if you managed to create a PDB file or not...