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Figure S1. Structures of the 25 CDK2 ligands with their PDB ID.

Figure S2. Superposition of the RRD and IFD docked ligand (green) with the experimental (PDB ID: 2C6O) conformation (gray) respectively: RM1A,B (RMSD = 1.73, 1.90), AM1C,D (RMSD (Å) = 1.19, 1.14), PM3E,F (RMSD (Å) = 1.13, 1.18), MNDO G,H (RMSD (Å) = 1.12, 1.15), DFT I,J (RMSD (Å) = 1.60, 1.22) and HF K,L (RMSD (Å) = 1.15, 1.33).

Table S1. CDK2 protein complexes used in the test set (25 CDK2 complexes) with their PDB ID, Resolution, Ki value, and number of rotatable bonds in respective complex compound.

Table S2. Average and descriptive analyses of RMSD from different docking performance calculation.

Table S3. RRD results with RMSD (Å) using different charges.

Table S4. IFD results with RMSD (Å) using different charges.

Table S5. RRD results with docking score (Kcal/mol) using different charges.

Table S6. IFD results with docking score (Kcal/mol) using different charges.

Table S7. Amino acid interaction in the active site of CDK2 by using RM1 charges.

Table S8. Amino acid interaction in the active site of CDK2 by using AM1 charges.

Table S9. Amino acid interaction in the active site of CDK2 by using PM3 charges.

Table S10. Amino acid interaction in the active site of CDK2 by using MNDO charges.

Table S11. Amino acid interaction in the active site of CDK2 by using DFT charges.

Table S12. Amino acid interaction in the active site of CDK2 by using HF charges.

Table S13. Hydrogen-bond-average distances (Å) between the inhibitors and hinge region of the CDK2 active site.

Table S14. RRD results from Prime MM-GBSA free energy of binding (ΔGbind) with experimental free energy of binding (ΔGexp) using different charges.

Table S15. IFD results from Prime MM-GBSA free energy of binding (ΔGbind) with experimental free energy of binding (ΔGexp) using different charges.

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