Docking result not same as reference structure

Hi. I am using easy inteface to do docking to dock my protein structure (tubulin) with small ligand (taxol). The PDB i used is IJFF.

First, i extract the chain B and cut the taxol ligand and save as two new PDB file using discovery studio. Then, for the active residue i just input the residue number based on the amino acid residue involved in interaction just as listed in PDBSum. (

That is Chain b: 23,26,27,233,236,369,360,370,276,275,274,230,229,292,278. For passive residue,i just tick the define automatically.

However, from the result i get. ( )
All the structure from the two cluster do not match with my reference structure in residue number interaction using ligplot.


May i know what is possible the mistake i have done. Is it because of the wrong active residue of input? Would appreciate if anyone can kindly advice and explain.

So basically you want to reproduce the crystal structure from its separated components? (I.e. a bound docking experiment).

Please have a look at the recommended settings for protein-ligand docking on our tutorial web page. And in particular refer to stage2 (setting up a new docking run targeting the identified binding pocket).

Docking has its limitations and there is no warranty you will get exactly the same structure. And taxol is a rather large and complex molecule.
Further you should always analyse multiple solutions/clusters.