Skip to main content

Table 4 Top 19 and 18 amino acid residues that interacted with the ligands in at least one snapshot for each of the three FFR models during the docking simulations

From: Effect of the explicit flexibility of the InhA enzyme from Mycobacterium tuberculosis in molecular docking simulations

(a) InhA_WT - ETH InhA_I16T - ETH InhA_I21V - ETH
Residue Best FEB Best Pose Best FEB Best Pose Best FEB Best Pose
  HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB
GLY14 681 363 64 47 89 80 2 2 1,652 311 264 18
ILE15 12 164 0 0 81 41 0 0 487 39 0 0
SER20 0 856 0 100 3 0 0 6 2 99 0 0
ILE21 0 1,015 0 1,974 0 971 0 1,528 0 0 0 0
VAL21 0 0 0 0 0 0 0 0 0 714 0 1,022
PHE41 0 4 0 0 0 65 0 0 0 426 0 0
SER94 1,115 955 387 740 1,311 516 156 762 1,712 1,683 447 1,060
ILE95 323 389 392 229 713 479 74 424 110 1,566 230 617
GLY96 178 169 2 213 8 781 0 124 2 270 0 170
MET147 10 1,127 49 1,805 3 755 9 943 2 849 3 1,096
ASP148 78 394 556 587 328 512 842 348 90 104 444 537
PHE149 5 1,028 0 1,235 0 1,529 0 1,531 0 564 0 1,453
MET161 0 1,064 0 1,664 1 1,204 0 1,838 2 712 0 1,675
LYS165 0 405 0 719 0 531 0 618 0 32 0 161
ALA191 4 184 16 666 0 177 12 707 42 90 55 483
GLY192 779 68 903 155 959 140 1,586 136 564 210 1,716 384
PRO193 0 333 0 305 0 398 0 256 0 408 0 720
ILE194 275 71 0 221 27 366 10 999 5 12 73 185
THR196 71 216 4 322 0 644 0 889 2 363 0 693
(b) InhA_WT - TCL InhA_I16T - TCL InhA_I21V - TCL
Residue Best FEB Best Pose Best FEB Best Pose Best FEB Best Pose
  HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB
GLY14 861 934 523 59 101 533 18 5 1,157 1,131 582 114
ILE16 0 494 0 85 0 0 0 0 0 571 0 191
THR16 0 0 0 0 0 433 0 38 0 0 0 0
ILE21 0 998 0 2,067 0 944 0 1,060 0 0 0 0
VAL21 0 0 0 0 0 0 0 0 0 638 0 1,200
PHE41 0 47 0 0 0 519 0 0 0 1,383 0 5
SER94 1,746 1,676 1,780 1,340 1,450 605 1,213 67 638 458 777 297
ILE95 241 562 342 450 645 1,134 259 108 438 1,022 249 242
GLY96 370 897 49 745 517 1,148 64 831 197 970 19 665
PHE97 26 71 13 103 17 31 26 1,430 2 70 7 125
MET103 2 9 0 0 0 0 0 0 13 33 105 1,370
MET147 121 541 137 910 13 507 8 268 13 257 8 341
PHE149 10 97 1 287 0 3 0 0 0 2 0 0
MET161 30 1,262 13 2,310 9 1,234 13 1,872 3 322 13 1,402
LYS165 0 176 0 570 0 111 0 203 0 0 0 2
GLY192 1,418 0 1,959 2 860 0 1,308 0 297 0 1,302 1
ILE194 1 0 8 3 2 152 6 1,830 13 0 21 17
THR196 16 55 40 269 0 276 6 438 2 86 1 499
(c) InhA_WT - PIF InhA_I16T - PIF InhA_I21V - PIF
Residue Best FEB Best Pose Best FEB Best Pose Best FEB Best Pose
  HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB HHB NNB
GLY14 83 202 57 103 1 125 2 0 65 818 15 379
ILE16 0 765 0 595 0 0 0 0 0 228 0 147
THR16 0 0 0 0 0 701 0 846 0 0 0 0
ILE21 0 456 0 1,370 0 333 0 865 0 0 0 0
VAL21 0 0 0 0 0 0 0 0 0 669 0 1,547
ASP42 14 10 1 10 671 553 53 0 17 13 2 7
PHE93 1 1,050 0 0 0 0 3 7 0 0 0 0
SER94 238 386 174 1,047 170 297 71 1,043 47 1,223 79 1,952
ILE95 2 773 9 1,779 191 565 65 1,275 0 1,942 1 2,202
GLY96 316 1,252 130 2,389 911 1,110 270 1,894 1,532 1,325 333 2,291
PHE97 1 1,050 7 1,146 3 757 0 531 1 186 0 166
PHE149 0 246 0 640 0 121 0 0 0 58 0 78
MET161 0 494 1 1,491 3 854 1 1,021 0 1,436 5 1,739
LYS165 0 160 0 303 0 347 0 0 0 12 0 20
GLY192 279 1 759 3 189 9 661 14 468 21 886 31
ILE194 11 5 55 7 4 67 9 335 17 78 25 355
THR196 4 472 14 1,295 6 905 10 1,491 38 2,168 16 2,572
LEU197 3 430 0 167 4 285 0 0 5 14 0 7
ALA198 0 382 0 735 0 105 0 0 1 11 0 21
  1. The first columns show, from the total of amino acid residues found in Table 3, the top 19 (18 for TCL) residues that were able to make contacts, HHB and/or NNB, with the ligands (a) ETH, (b) TCL, and (c) PIF, respectively, in at least 10% of the trajectories. Note that each FFR model is a MD simulation trajectory. Columns 2 to 13 show the number of snapshots for each FFR model involved in such contacts (marked in bold).