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Table 1 Collection of 48 complexes and their corresponding apo-forms to evaluate pocket prediction results.

From: PocketPicker: analysis of ligand binding-sites with shape descriptors

Complex Unbound Protein Description Pocket Ligand1 Other Ligands2
1bid 3tms Thymidylate synthase UMP CBX
1cdo 8adh Alcohol dehydrogenase NAD zn
1dwd 1hxf Alpha thrombin MID chains i, l
1fbp 2fbp Fructose 1,6-bisphosphatase AMP F6P, mg
1gca 1gcg Glucose/galactose-binding protein GAL ca
1hew 1hel Hen egg white lysozyme NAG -
1hyt 1npc Thermolysin BZS DMS, ca, zn
1inc 1esa Elastase ICL ca, so4
1rbp 1brq Retinol binding protein RTL -
1rob 8rat Ribonuclease A C2P -
1stp 1swb Streptavidin BTN -
1ulb 1ula Purine nucleoside phosphorylase GUN so4
2ifb 1ifb Fatty acid binding protein PLM -
3ptb 3ptn Beta trypsin BEN ca
2ypi 1ypi Triose phosphate isomerase PGA -
4dfr 5dfr Dihydrofolate reductase MTX ca, cl
4phv 3phv HIV 1 protease VAC -
5cna 2ctv Concanavalin A MMA ca, cl, mn
7cpa 5cpa Carboxypeptidase A FVF zn
1a6w 1a6u B1-8 FV fragment NIP -
1acj 1qif Acetylcholinesterase THA -
1apu 3app Penicillopepsin [IVA-VAL-VAL-STA-OET] MAN
1blh 1djb Beta-lactamase FOS -
1byb 1bya Beta amylase GLC so4
1hfc 1cge Fibroblast collagenase HAP ca, zn
1ida 1hsi HIV 2 protease [QND-VAL-HPB-PPL-PY2] -
1igj 1a4j Immunoglobulin DGX chain y
1imb 1ime Inositol monophosphatase LIP gd
1ivd 1nna Hydrolase ST1 FUC, NAG, MAN, ca
1mrg 1ahc Alpha momorcharin ADN -
1mtw 2tga Trypsin DX9 ca
1okm 4ca2 Carbonic anhydrase II SAB hg, zn
1pdz 1pdy Enolase PGA ace, mn
1phd 1phc Camphor 5-monoxygenase PIM HEM
1pso 1psn Pepsin 3a [IVA-VAL-VAL-STA-ALA-STA] -
1qpe 3lck Lck kinase PP2 PTR, so4
1rne 1bbs Renin C60 NAG
1snc 1stn Staphylococcal nuclease PTP ca
1srf 1pts Streptavidin MTB -
2ctc 2ctb Carboxypeptidase A LOF zn
2h4n 2cba Carbonic anhydrase II AZM zn
2pk4 1krn Plasminogen kringle ACA -
2sim 2sil Sialidase DAN -
2tmn 1l3f Thermolysin [PHO-LEU-NH2] ca, zn
3gch 1chg Gamma chymotrypsin CIN -
3mth 6ins Methylparaben insulin MPB cl, zn
5p2p 3p2p Phosphilipase DHG ca
6rsa 7rat Ribonuclease A UVC dod
  1. 1Considered ligand defining the active site. Brackets indicate ligands composed of multiple residues or fragments.
  2. 2Additional ligands and ions were removed prior to computations.