Protein-ligand binding pocket

Protein-ligand binding pocket#

Identification of protein-ligand binding pockets is crucial for understanding many biological processes that is mediated by ligands and its visualization can help drug discovery and biological interpretation. TMKit allows users to show the pocket details of a protein-ligand complex.

Reminder of data

Please make sure that the build-in example dataset has been downloaded before you walk through the tutorial.

Example usage#

The protein structure 6feq is a transmembrane protein-ligand complex, showing a structure of inhibitor-bound human multidrug transporter ABCG2 (as shown in the plot below). A small molecule inhibitor (or ligand) Ko143 can inhibition the biological functions of ABCG2. We extract the complex structure and show the protein-ligand pocket in multiple forms . The complex has been placed in data/example/vs/.

../../../_images/6feq.png

Caption: Protein-ligand complex of 6feq#

First, we can visualize it in rainbow form annotated with residues around the ligand using the following code.

import tmkit as tmk

tmk.vs.sm_local(
    prot_name='6feq',
    pdb_complex_fp=to('data/example/vs/'),
    sm_rep="sticks",
    nby_rep='sticks',
    prot_c='blue_white_magenta',
    sm_c='blue_green',
    pocket_rep='stick'
)
../../../_images/rainbow.png

Caption: Close-up of the binding pocket in rainbow form.#

Second, we can visualize it in sphere form with no residue annotation using the following code.

import tmkit as tmk

tmk.vs.sm_local(
    prot_name='6feq',
    pdb_complex_fp='data/pdb/rcsb/',
    sm_rep="sticks",
    nby_rep='sticks',
    prot_c='blue_white_magenta',
    sm_c='blue_green',
    pocket_rep='sphere'
)
../../../_images/sphere.png

Caption: Close-up of the binding pocket in sphere form.#

Third, we can visualize it in surface form with no residue annotation using the following code.

import tmkit as tmk

tmk.vs.sm_local(
    prot_name='6feq',
    pdb_complex_fp='data/pdb/rcsb/',
    sm_rep="sticks",
    nby_rep='sticks',
    prot_c='blue_white_magenta',
    sm_c='blue_green',
    pocket_rep='surface'
)
../../../_images/surface.png

Caption: Close-up of the binding pocket in surface form.#

Attributes#

Attribute

Description

prot_name

name of a protein in the prefix of a PDB file name (e.g., 1xqf in 1xqfA.pdb)

pdb_complex_fp

path where a target protein complex file is place

prot_c

color of the entire protein

sm_rep

representation of a ligand

nby_rep

representation of amino acid residues surrounding a ligand

sm_c

color of a ligand

See also

Please see here for better understanding the file-naming system.

Output#

Finally, you will see the following output.

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 Detected OpenGL version 4.6. Shaders available.
 Detected GLSL version 4.60.
 OpenGL graphics engine:
  GL_VENDOR:   NVIDIA Corporation
  GL_RENDERER: NVIDIA GeForce RTX 2070/PCIe/SSE2
  GL_VERSION:  4.6.0 NVIDIA 536.40
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