2020 DOCK tutorial 3 with PDBID 4F4P

This tutorial teaches you how to dock a drug molecule to a receptor.

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I. Introduction

4F4P

4F4P is the crystal structure of Tyrosine Kinase SYK in complex with ligand LASW836. You can get the pdb file from here [1]. The resolution is 2.37 Å

Checking the structure

Read the article related to the PDB file [2] to understand protonation states, charges, environmental conditions and other important information regarding the receptor and the ligand.

Open the pdb file through chimera and look at the structure.

Identify the main components of the model (receptor, ligand, solvent, cofactors). In our case, the protein contain one chain, ligand and sulfate(SO_4).

Prepare the Receptor file

In this part we are going to generate the receptor file and the ligand file that will going to be used in docking by chimera.

As you have seen, the pdb file is not very clean. We need to do some modifications to make it suitable for docking studies. With the pdb file loaded by chimera, do Select -> Residue -> SO4 to select the sulfate. Use Actions -> Atoms/Bonds -> Delete to delete it. Then do Select -> Residue -> HOH to select the water molecules. Use the same method to delete it. Then do Select -> Structure -> ligand to select ligand molecule. Use the same method to delete it. Save the receptor as 4f4p_rec_noh.mol2.

[[File:]]

Prepare the Ligand File

Open the pdf file again. Do Select -> Structure -> ligand to select the ligand. Do Select -> Invert (all models), then delete the selected atoms. This will left the ligand molecule only. Save it as 4f4p_lig_noh.mol2.

[[File:]]

Adding hydrogen and charge

Now we are going to add hydrogen atoms and charges to our receptor and ligand. Open 4f4p_rec_noh.mol2 file again using Chimera and use the following instructions to prepare the receptor file to be used in DOCK.

Open 2p16_noh_lig.mol2, follow the same steps for rec file, add hydrogen and charges, and save the file as 2p16_wh_lig.mol2.