Molecular Docking Dataset for Native Ligand Validation (38Z/SCH772984) on Wild-Type Human MAPK3/ERK1 (PDB ID: 4QTB)

This dataset contains the complete input, output, parameter configurations, and structural analysis files for the native ligand redocking validation on wild-type Human Mitogen-Activated Protein Kinase 3 (MAPK3/ERK1, PDB ID: 4QTB). The validation was conducted in independent triplicates (3 test runs) using AutoDock4 to establish the accuracy, repeatability, and convergence of the docking protocol prior to virtual screening. Macromolecule and Ligand InformationProtein Target: Wild-Type Homo sapiens MAPK3 (PDB ID: 4QTB, Resolution: 1.40 Å)Native Ligand: 38Z/SCH772984 (PubChem Compound Identifier (PCID): 24866313)Crystallization Method: X-Ray Diffraction Grid Box Coordinates & ParametersGrid Center (X, Y, Z): 34.977, 56.722, 50.362Grid Points (X, Y, Z): 58, 42, 46 (Total: 119,239 points)Grid Spacing: 0.375 Å Lamarckian Genetic Algorithm (LGA) SettingsNumber of Genetic Algorithm Runs: 100 runs per testPopulation Size: 150Maximum Number of Energy Evaluations: 10,000,000 (Medium)Maximum Number of Generations: 27,000 Summary of Triplicate Validation Results (Mean ± SD)Reference RMSD: 0.6533 ± 0.2542 Å (Coefficient of Variation: 38.9129%) — Conclusion: PASSED (< 2.0 Å)Lowest Binding Energy (ΔG): -17.49 ± 0.0666 kcal/mol (Coefficient of Variation: 0.3806%) — Conclusion: PASSEDEstimated Inhibition Constant (Ki): 150.93 ± 16.5253 femtomolar (fM) (Coefficient of Variation: 10.9490%) — Conclusion: PASSEDFirst Rank Cluster Population: 22.67 ± 2.5166% (Coefficient of Variation: 11.1027%) — Conclusion: PASSED Key Conserved Residue InteractionsAll triplicate runs consistently showed crucial conventional hydrogen bonds with key hinge region and catalytic residues (MET125, LYS71, LYS131, ASP123), along with hydrophobic Pi-Pi stacking with TYR81 and Pi-Alkyl interactions with VAL56, ALA69, ILE73, ARG84 and LEU173. Contents of the Dataset1. .gpf and .dpf for grid and docking parameter input files.2. .pdbqt for prepartum receptor and ligand structures.3. .dlg for AutoDock output log files for all triplicate runs.4. .pdb for extracted best pose binding models and complex visualization.5. .png and .jpg for 2D and 3D visualization of amino acid interactions.6. .pdf for complete structured summary table and 2D/3D interaction maps. License & ReusabilityThis dataset is published under the Creative Commons Attribution 4.0 International (CC BY 4.0) license. Researchers are free to reuse, modify, and benchmark these data for computational drug discovery targeting MAPK3.