Skip to main content

Advertisement

Table 1 Experimental data for the 54 protein-ligand complexes.

From: Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock

PDB code Protein Res (Å) Ligand Structure Ref.
1AI5 Penicillin acylase 2.4 m-nitrophenylacetic acid [24]
1AJP Penicillin acylase 2.3 2,5-dihydroxyphenylacetic acid [24]
1AMW Heat shock protein 90 1.9 ADP [25]
1BGQ Heat shock protein 90 2.5 radicicol [26]
1CBR Retionic acid binding protein 2.9 retinoic acid [27]
1D3Q Human thrombin 2.9 benzo [b]thiophene derivative [28]
1D3T Human thrombin 3.0 benzo [b]thiophene derivative [28]
1DWB a-Thrombin 3.2 benzamidine [29]
1FLR Immunoglobulin 1.9 fluorescein [30]
1GNI Human serum albumin 2.4 oleic acid [31]
1HVJ HIV-1 Protease 2.0 A78791 [32]
1HVR HIV-1 Protease 1.8 XK263 [33]
1K4G tRNA-guanine transglycosylase 1.7 quinazoline derivative [34]
1KV1 p38 MAP kinase 2.5 pyrazol derivative [35]
1LIF Adipocyte lipid-binding protein 1.6 stearic acid [36]
1M0N Dialkylglycine decarboxylase 2.2 1-aminocyclo-pentanephosphonate [37]
1M0Q Dialkylglycine decarboxylase 2.0 S-1-amino-ethanephosphonate [37]
1OLU Branched-chain alpha-ketoacid dehydrogenase kinase 1.9 thiamin diphosphate [38]
1Q8T cAMP-dependent protein kinase 2.0 (R)-trans-4-(1-aminoethyl)-n-(4-pyridyl) cyclohexanecarboxamide [39]
1RBP Retinol-binding protein 2.0 retinol [40]
1S39 tRNA-guanine transglycosylase 2.0 2-aminoquinazolin-4(3H)-one [41]
1U33 Alpha-amylase 2.0 5-trihydroxy-6-hydroxymethyl-piperidin-2-one [42]
1ULB Purine nucleoside phosphorylase 2.8 guanine [43]
1UWT Beta-glycosidase 2.0 D-galactohydroximo-1,5-lactam [44]
1X8R 3-Phosphoshikimate 1-carboxyvinyltransferase 1.5 phosphonate analogue [45]
1XD1 Alpha-amylase 2.2 acarbose derived hexasaccharide [46]
1YDT cAMP-dependent protein kinase 2.3 n-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline [47]
1ZC9 Dialkylglycine decarboxylase 2.0 pyridoxamine 5-phosphate [48]
2ACK Acetylcholinesterase 2.4 edrophonium ion [49]
2BAJ p38alpha Map kinase 2.3 pyrazol derivative [50]
2BAK p38alpha Map kinase 2.2 nicotinamid derivative [50]
2CEQ Beta-glycosidase 2.1 glucoimidazole [51]
2CET Beta-glycosidase 2.0 phenethyl-substituted glucoimidazole [51]
2CGR Immunoglobulin 2.2 N-trisubstituted guanidine [52]
2CPP Cytochrome P-450cam 1.6 camphor [53]
2D3U RNA-dependent RNA polymerase 2.0 non-nucleoside analogue inhibitor I [54]
2D3Z RNA-dependent RNA polymerase 1.8 non-nucleoside analogue inhibitor II [54]
2FDP Beta-secretase 2.5 amino-ethylene inhibitor [55]
2G94 Beta-secretase 1.9 valinamide derivative [56]
2GBP D-galactose/D-glucose binding protein 1.9 glucose [57]
2IFB Fatty-acid-binding protein 2.0 palmitic acid [58]
2IWX Heat shock protein 82 1.5 synthetic macrolactone [59]
2J77 Beta-glycosidase 2.1 deoxynojirimycin [Gloster, to be published]
2J78 Beta-glycosidase 1.7 gluco-hydroximolactam [Gloster, to be published]
2QFU 3-Phosphoshikimate 1-carboxyvinyltransferase 1.6 shikimate-3-phosphate [60]
2QWB Neuraminidase 2.0 sialic acid [61]
2QWD Neuraminidase 2.0 4-amino-Neu5Ac2en [61]
2R04 Rhinovirus 14 coat protein 3.0 W71, antiviral agent [62]
2XIS Xylose isomerase 1.6 D-xylitol [63]
2YPI Triose phosphate isomerase 2.5 2-phosphoglycolic acid [64]
3PTB b-Trypsin 1.8 benzamidine [65]
4HMG Hemagglutinin 3.0 sialic acid [66]
7ABP Arabinose-binding protein 1.7 fucose [67]