Table 2 Simultaneously Interacting Residues of 1000 compounds.

From: Identification of potential modulators for human GPD1 by docking-based virtual screening, molecular dynamics simulations, binding free energy calculations, and DeLA-drug analysis

Rank

Residue 1

Residue 2

Residue 3

Residue 4

Residue 5

Ligand percentage

1

B:TRP14

B:PRO94

B:LYS120

B:LYS204

B:ARG269

5.10%

2

B:PRO94

B:LYS120

B:LYS204

B:ARG269

B:LYS296

3.60%

3

B:VAL92

B:PRO94

B:LYS120

B:LYS204

B:ARG269

3.40%

4

B:PRO94

B:LYS120

B:ILE152

B:LYS204

B:ARG269

3.30%

5

B:TRP14

B:PRO94

B:LYS120

B:ILE152

B:ARG269

3.20%

6

B:PRO94

B:LYS120

B:LYS204

B:ARG269

 

25.60%

7

B:TRP14

B:PRO94

B:LYS120

B:ARG269

 

24.10%

8

B:TRP14

B:LYS120

B:LYS204

B:ARG269

 

19.60%

9

B:TRP14

B:PRO94

B:LYS204

B:ARG269

 

18.10%

10

B:TRP14

B:PRO94

B:LYS120

B:LYS204

 

17.10%

11

B:PRO94

B:LYS120

B:ARG269

  

62.30%

12

B:LYS120

B:LYS204

B:ARG269

  

48.30%

13

B:PRO94

B:LYS204

B:ARG269

  

46.90%

14

B:TRP14

B:LYS120

B:ARG269

  

45.60%

15

B:PRO94

B:LYS120

B:LYS204

  

45.30%

16

B:PRO94

B:ARG269

   

76.30%

17

B:LYS120

B:ARG269

   

75.40%

18

B:PRO94

B:LYS120

   

68.00%

19

B:LYS204

B:ARG269

   

56.20%

20

B:TRP14

B:ARG269

   

54.40%

  1. This table presents twenty sets of data, each consisting of five residues. These residues represent the most common combinations observed in the binding conformational analysis of 1000 molecules. The percentage indicates the frequency of occurrence of each residue combination among all the possible binding configurations. For instance, in rank 1, the five residues are present in 5.1% of all conformations. Notably, in rank 16, two residues, PRO94 and ARG269, are present in 76.3% of conformations, indicating their high prevalence and significance in the binding interactions.