Project Report: Docking site of Dopamine onto D4 Receptor using AutoDock Vina
1. Objective
The main goal of this project was to identify and visualize the docking site of dopamine on the D4
receptor using AutoDock Vina and PyMOL.
2. Methodology
Step 1. Receptor Preparation
• The D4 receptor structure was downloaded from the Protein Data Bank (PDB).
• The structure was cleaned (removal of water molecules, heteroatoms, and unnecessary
chains).
• File was saved as receptor_clean.pdb.
• Using AutoDock Tools (ADT), polar hydrogens were added and Gasteiger charges assigned.
• The receptor was then converted to docking format → receptor6.pdbqt.
Step 2. Ligand Preparation
• Dopamine structure was obtained in SDF format (datadopamine.sdf).
• Converted to PDB format using OpenBabel → dopamine.pdb.
• In AutoDock Tools, torsions and rotatable bonds were defined, and the ligand was saved as
dopamine_single.pdbqt.
• Multiple poses were avoided by ensuring single model export.
Step 3. Defining the Docking Grid
• Binding site coordinates were set based on cavity analysis:
• center_x = 108.988
• center_y = 94.237
• center_z = 101.784
• size_x = 20
• size_y = 20
• size_z = 20
• These parameters were stored in config.txt.
Step 4. Running AutoDock Vina
• The docking was executed using the following command:
• vina --receptor receptor6.pdbqt --ligand dopamine_single.pdbqt --config config.txt --out
out.pdbqt --log log.txt
• Output files generated:
o out.pdbqt → docked ligand poses
o log.txt → binding affinity results
Step 5. Visualization in PyMOL
• Receptor and docked ligand were loaded in PyMOL:
• load receptor6.pdbqt
• load out.pdbqt
• Pocket residues within 4 Å of dopamine were highlighted:
• select ligand, out
• select pocket, (receptor6 within 4 of ligand)
• show sticks, ligand
• color yellow, ligand
• show sticks, pocket
• color cyan, pocket
• show surface, receptor6
• set transparency, 0.45, receptor6
• distance hbonds, ligand, pocket, 3.2
• label pocket and name CA, "%s%s" % (resn, resi)
3. Results
Docking Score
• The best binding pose (MODEL 1) showed an estimated binding affinity of:
-5.2 kcal/mol (from log.txt).
Docking Site
• Dopamine (yellow sticks) docked in the predicted binding pocket of the D4 receptor.
• Pocket residues (cyan sticks) surrounding dopamine included amino acids such as ASP, TYR,
SER, and PHE (actual residue numbers labeled in PyMOL).
• Hydrogen bonds and hydrophobic contacts stabilized the binding.
Insert PyMOL figures here:
1. Surface view showing receptor cavity with dopamine inside.
2. Stick view highlighting dopamine and surrounding residues with labels.
3. Interaction diagram (if generated via LigPlot/PLIP).
4. Discussion
• The docking results confirm that dopamine binds within the expected cavity of the D4
receptor.
• The predicted interactions (H-bonds with polar residues, π-stacking with aromatic residues)
are consistent with known catecholamine receptor interactions.
• A binding energy of ~ -5 kcal/mol indicates moderate binding affinity, which is typical for
neurotransmitter-receptor docking.
5. Conclusion
• The project successfully demonstrated the docking of dopamine onto the D4 receptor.
• The docking site was visualized using PyMOL, and key interacting residues were identified.
• This workflow provides a basic but complete molecular docking pipeline:
Structure preparation → Docking → Visualization → Interaction analysis.
6. References
1. Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking
with a new scoring function, efficient optimization, and multithreading. Journal of
Computational Chemistry, 31(2), 455–461.
2. The PyMOL Molecular Graphics System,
3. AutoDock Vina official
