Ligand Binding Cavities & Docking

Question

[KS]

For my school project I need to find if curcumin has binding sites in P01106 (UniProt ID). My steps were 1)build a model 2)find ligand biding sites(castP) 3)find structural coordinates of curcumin 4)Molecular Docking using AutoDock

I found a 3D model for this protein in modbase and I also constructed a new model using SWISS-MODEL which is very similar to modbase model

I am trying to find ligand binding cavities within the above model using castP server. But I am not sure how exactly to start with?

How to find coordinates of curcumin?

Answer 1

[dimkal]

to find curcumin binding site you might want to look where other ligands bind to the proteins that related to P01106. See if there's a cocrystal of your template with another ligand, likely the binding site will be the same.

I tried to see if PDB repository has coordinates for curcumin but it doesn't. so I went ahead and generated the molecule based on its SMILES string found on wikipedia page: O=C(\C=C\c1ccc(O)c(OC)c1)CC(=O)\C=C\c2cc(OC)c(O)cc2

I used Schrodinger's LigPrep to go from 1D to 3D. The PDB coordinates can be found here

and good luck on your project.