Table II.
Protein Codeb | Name | AA Countc | Water Countd | Apo structuree | RMS (Å)f | Ligand Code (j) | Nameg | Volume (Å3) | Categorya |
---|---|---|---|---|---|---|---|---|---|
PDB codes | |||||||||
1b70 | phenylalanyl tRNA synthetase | 1039 | 134 | 1pys | 0.42 | 1 | phenylalanine | 203 | BD-passed |
1cea | recombinant kringle 1 domain of human plasminogen | 79 | 148 | 1pkr | 0.50 | 1 | aminocaproic acid | 181 | Drug complex |
1dy4 | cellobiohydrolase I | 434 | 342 | 1cel | 0.30 | 1 | s-Propranolol | 338 | BD-failed |
2a | NAG 435 | 240 | |||||||
2b | NAG 436 | 240 | |||||||
1e7a | human serum albumin | 577 | 120 | 1ao6 | 0.89 | 1a | propofol 4001 | 255 | BD-failed |
1b | propofol 4002 | 255 | |||||||
1eqg | prostaglandin h2 synthase-1 | 550 | 251 | 1prh | 0.38 | 1 | Ibuprofen | 294 | BD-failed |
2a | NAG 661 | 240 | |||||||
2b | NAG 681 | 240 | |||||||
2c | NAG 662 | 240 | |||||||
2d | NAG 671 | 240 | |||||||
2e | NAG 1672 | 240 | |||||||
3a | BOG 802 | 383 | |||||||
3b | BOG 801 | 383 | |||||||
4 | HEME | 732 | |||||||
1h61 | pentaerythritol tetranitrate reductase | 364 | 545 | 1h50 | 0.21 | 1 | prednisone | 427 | Drug complex |
2 | FMN | 456 | |||||||
1hvy | human thymidylate synthase | 287 | 596 | 1hw3 | 0.77 | 1 | Raltitrexed (Tomudex) | 521 | Drug complex |
2 | UMP (covalently bound) | 293 | |||||||
1hz4 | transcription factor malt domain iii | 366 | 408 | 1 | benzoic acid | 147 | BD-failed | ||
2 | GOL | 114 | |||||||
1ivb | influenza virus b/lee/40 neuraminidase | 390 | 0 | 1 | 4-(acetylamino)- 3-hydroxy- 5-nitrobenzoic acid | 245 | BD-failed | ||
2 | NAG | 240 | |||||||
1ju4 | cocaine esterase | 569 | 436 | 3i2j | 0.22 | 1 | benzoic acid | 147 | BD-failed |
1lna | thermolysin | 316 | 158 | 1l3f | 0.62 | 1 | Val-Lys | 322 | BD-failed |
1m2z | human glucocorticoid receptor ligand-binding domain | 254 | 205 | 1 | Dexamethasone | 459 | Drug complex | ||
2a | BOG 501 | 383 | |||||||
2b | BOG 778 | 383 | |||||||
2c | BOG 779 | 383 | |||||||
1ngp | n1g9 (igg1-lambda) fab fragment | 431 | 131 | 1ngq | 0.29 | 1 | 2-(4-hydroxy-3- nitrophenyl) acetic acid | 204 | BD-failed |
1pth | prostaglandin h2 synthase-1 | 550 | 1 | 1prh | 0.36 | 1 | salicylic acid | 158 | BD-failed |
2a | NAG 661 | 240 | |||||||
2b | NAG 671 | 240 | |||||||
2c | NAG 672 | 240 | |||||||
2d | NAG 681 | 240 | |||||||
3 | BOG | 383 | |||||||
4 | HEME | 732 | |||||||
3pcn | protocatechuate 3,4-dioxygenase | 436 | 1374 | 2pcd | 0.39 | 1 | 2-(3,4-dihydroxy phenyl) acetic acid | 194 | BD-failed |
3tpi | trypsinogen-bpti complex | 287 | 152 | 1 | Ile-Val | 314 | BD-passed |
Categories of complexes according to previous investigations. BD-passed/BD-failed: BD of the ligand to the protein was successful/failed with AutoDock3 in the previous studies7,8. Drug complex: complexes with drug as ligand molecule bound to protein.
Protein code used as a reference in this study for both the holo and apo target forms (identical to the PDB ID of the holo conformation of the protein).
Number of amino acid residues in the protein target.
Number of crystallographic water molecules found in the holo PDB file and used for evaluation.
PDB ID of the primary-ligand-free (apo) conformation of the protein target (not used as a reference code in the text).
Root Mean Square Deviation between the Cα atoms of the holo and apo conformations of the target protein.
Abbreviated names of ligand molecules. NAG: N-acetyl-d-glucosamine. BOG: β-octylglucoside. FMN: flavin mononucleotide. GOL: glycerol. UMP: 2′-deoxyuridine 5′-monophosphate.