Table 4.
The PDB structures employed for ligands present in dissimilar bound conformations in different receptors
| Namea | Rotorsb | RMSD differencesc (Angstroms, Å) | RMSD pre/post-minimizationd (Angstroms, Å) | Number of conformers | Minimum RMSD (Angstroms, Å) | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| omega e | nmrclust f | rms g | rms_avg h | omega e | nmrclust f | rms g | rms_avg h | ||||
| pbn_1TNI | 4 | 1.386 | 0.44 | 39 | 8 | 9 | 7 | 0.48 | 0.664 | 0.48 | 0.48 |
| pbn_1UTP | 4 | 0.312 | 39 | 8 | 9 | 7 | 0.507 | 0.63 | 0.761 | 0.761 | |
| pt1_1BR6 | 4 | 2.107 | 0.308 | 78 | 15 | 15 | 19 | 0.613 | 1.121 | 0.794 | 0.794 |
| pt1_1TX0 | 4 | 0.513 | 78 | 15 | 15 | 19 | 0.894 | 1.112 | 1.107 | 0.966 | |
| adp_13PK | 6 | 2.193 | 1.134 | 500 | 65 | 68 | 180 | 1.132 | 1.154 | 1.192 | 1.192 |
| adp_1HW8 | 6 | 0.862 | 500 | 65 | 68 | 180 | 1.435 | 1.486 | 1.441 | 1.363 | |
| kan_1KNY | 6 | 2.248 | 0.709 | 500 | 41 | 45 | 70 | 1.855 | 1.855 | 2.039 | 2.039 |
| kan_1L8T | 6 | 0.626 | 500 | 41 | 45 | 70 | 2.026 | 2.026 | 1.764 | 1.815 | |
| i84_1EKO | 8 | 1.369 | 0.519 | 500 | 62 | 69 | 50 | 1.124 | 1.149 | 1.217 | 1.609 |
| i84_1EL3 | 8 | 0.383 | 500 | 62 | 69 | 50 | 0.891 | 0.947 | 0.962 | 0.997 | |
| fad_1A8P | 13 | 2.851 | 0.656 | 500 | 40 | 48 | 500 | 1.634 | 1.746 | 2.288 | 1.634 |
| fad_1B2R | 13 | 0.605 | 500 | 40 | 48 | 500 | 2.116 | 2.363 | 2.169 | 1.574 | |
| acd_1ADL | 14 | 1.859 | 0.667 | 500 | 64 | 69 | 148 | 1.081 | 1.081 | 1.081 | 1.081 |
| acd_1CVU | 14 | 0.57 | 500 | 64 | 69 | 148 | 1.306 | 1.532 | 1.494 | 1.435 | |
| im1_1SBG | 16 | 3.306 | 0.357 | 500 | 68 | 75 | 75 | 1.576 | 1.595 | 1.76 | 1.76 |
| im1_1TCW | 16 | 0.414 | 500 | 68 | 75 | 75 | 1.732 | 1.732 | 1.665 | 1.665 | |
| L95 | 6.422 | 1.607 | 0.452 | 284.277 | 33.242 | 36.545 | 48.531 | 0.997 | 1.128 | 1.106 | 1.087 |
| Mean | 8.875 | 2.165 | 0.567 | 389.625 | 45.375 | 49.750 | 131.125 | 1.275 | 1.387 | 1.388 | 1.323 |
| U95 | 11.328 | 2.723 | 0.683 | 494.973 | 57.507 | 62.954 | 213.719 | 1.554 | 1.646 | 1.671 | 1.558 |
| Standard deviation | 4.60 | 0.67 | 0.22 | 197.70 | 22.77 | 24.78 | 155.00 | 0.52 | 0.49 | 0.53 | 0.44 |
The statistics of the data are shown in the last four rows of the table
aThe name of the ligands and protein databank IDs are represented by the first three and last four alphanumeric characters, respectively
bThe number of rotatable bonds in the ligands
cRMSDs between the bound conformations of the same ligand in the two receptors selected
dThe RMSDs between the minimized and unminimized bound ligand conformation. More details are presented in the Methods section
eEnumerated with recommended settings in OMEGA
Generated by: f Clustering the OMEGA conformers employing the NMRCLUST algorithm
gAdjusting the rms parameter of OMEGA to generate similar numbers of conformers as the number of clusters identified by the NMRCLUST algorithm
hPartitioning the dataset into low, medium and large numbers of rotatable bonds, averaging the rms values in each group and using the averaged rms values. L95 and U95 are the lower and upper 95% confidence interval of the mean, respectively