Drawing the active site of an enzyme

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POCKET - program for drawing active site of an enzyme

Design of more efficient inhibitors and in particular drug design tasks are required to know the geometrical property of the active site of studied enzyme. One important feature of the substrate binding site in enzymes is the Van der Waals shape of this pocket. POCKET is a simple program for drawing of the enzyme active site. This program in compare with other similar programs builds the maximal space available for substrate rather than shape of the enzyme binding pocket.

Algorithm for drawing a protein binding site

For calculation of the shape of an enzyme binding pocket it is necessary to have the coordinates for protein molecule in PDB format. Furthermore it is important to have coordinates for at least one atom within binding pocket. This can be atoms from either inhibitor bound to the enzyme active site, or either just one water molecule from this binding pocket. If you do not have any atoms in the binding pocket, it is necessary to introduce one.

Algorithm for step-by-step enzyme binding site drawing

Shrink all non-enzyme atoms from the enzyme coordinates
Prepare PDB file with substrate coordinates. In none available make only one atom within the binding pocket - this atoms will be used as a reference point for binding pocket exploration.
Filling the spherical space around the protein binding pocket (on the basis of the coordinates from the previous step) with fine grid of probe atoms
Reject probe atoms lies within prohibited Van der Waals radii from the protein atoms.
Build a Van der Waals shape around probe atoms

Now we can do it on real structure in order to explain each step in details.

Example of step-by-step enzyme binding pocket drawing

For this example a structure of a triclosan binding enoyl reductase will be taken. For picture presentation it is possible to use any modern use any molecular graphics software. For our example we will use WebLab ViewerPro 4.0. Unfortunately the web site with WebLab ViewerPro software has been disappeared and we can't provide the reference to the official homepage.

Step 1: Split the PDB file of the substrate/enzyme complex into two files, with substrate (substrate.pdb) and enzyme with NAD⁺ (protein.pdb).

Step 2: Run the program POCKET as follow:
pocket.exe protein.pdb substrate.pdb 6 0.4 > res.pdb
Where 6 - is a radius of substrate extension in angstrom, 0.4 - exploration step in angstrom, res.pdb - final pdb file. Read bottom of the page about how to download this program.

Step 3: Load res.pdb into WebLab Viewer

enzyme pocket filling with grid of probe atoms

Step 4: With the select tool in WebLab Viewer delete all separated atoms.

Step 5: Draw the Van der Waals shape of the enzyme binding pocket:

Add the surface: Tools -> Surface -> Add and then select the resulting surface
Change the display style: View -> display style
Surface: VDW, Transparent, Color by: Atom Color -> Atom
Atom: Off -> Ok

Step 6: Load real substrate: Edit -> Paste from -> substrate.pdb-> Open

Step 7: Change substrate display style: View -> display style -> Stick -> Ok

Step 8: Load enzyme coordinates: Edit -> Paste from -> protein.pdb-> Open

Step 9: Change the enzyme display style: View -> display style -> display bond order (off) -> Stick -> Stick size (0.1) -> Ok

Step 10: Make NAD⁺ more visible: Select NAD⁺ molecule by double-click on the any of NAD⁺ atoms. View -> Display style -> Stick -> Stick size (0.2) -> Ok

Step 11: Draw the surface for the real substrate: Select substrate by double-click on any atoms. Tools -> Surface -> Add

Step 12: Change the substrate surface: Click once on the surface. If it is impossible, go to hierarchy window: Window -> New Hierarchy Window and in this window select you surface. Then View -> Display style -> VDW->Display as Wire Mesh -> Ok

Step 13: Select the best orientation by rotating, translating and scaling of your structure. Improve quality of the picture: View -> Options -> Lighting -> Light 2 -> Graphics -> Quality -> Ultra-high -> Ok

Step 14: Save final results: File -> Save. It is important to save in two formats: WebLab Viewer (*.msv) format - for further editing and in JPEG File (*.jpg) for publishing. When save in JPEG format the information about required resolution should be prompted. For most publishers the final size of 3000 pixel width with keeping aspect ration will be perfect.

Download program for drawing active site of an enzyme

pocket.exe	Windows 95, 98, NT, 2000, XP - executable file. Very likely proper operation under Windows Vista. Download into work directory, or into directory specified in PATH string.
pocket.exe.gz	Windows 95, 98, NT, 2000, XP - gzipped executable file. Very likely proper operation under Windows Vista. Download, unzip and place into work directory, or into directory specified in PATH string.