Skip to main content
. 2011 Mar 16;20(5):880–893. doi: 10.1002/pro.618

Table II.

Protein-Ligand Complexes used for Evaluation

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
a

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.

b

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).

c

Number of amino acid residues in the protein target.

d

Number of crystallographic water molecules found in the holo PDB file and used for evaluation.

e

PDB ID of the primary-ligand-free (apo) conformation of the protein target (not used as a reference code in the text).

f

Root Mean Square Deviation between the Cα atoms of the holo and apo conformations of the target protein.

g

Abbreviated names of ligand molecules. NAG: N-acetyl-d-glucosamine. BOG: β-octylglucoside. FMN: flavin mononucleotide. GOL: glycerol. UMP: 2′-deoxyuridine 5′-monophosphate.