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Table 4 Structures used in protein-ligand and protein-protein pocket analysis

From: Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets

Target protein (PDB id of apo structure) Inhibitor (PDB id) Protein partner (PDB id)
Bcl-X L ) acyl sulfonamide derivative Bak
(1LXL) (1YSI) (1BXL)
MDM2 benzodiazapine derivative p53
(1Z1M) (1T4E) (1YCR)
Xiap apoptosis inhibitor naphthalenamide derivative Caspase 9
Bir3 domain (1F9X) (1TFQ) (1NW9)
Xiap apoptosis inhibitor Smac peptidomimetic SMAC caspase activator
Bir3 domain (1F9X) (2JK7) (1G73)
ZipA indoloquinolizin inhibitor 1 FtsZ
(1F46) (1S1J) (1F47)
HPV11 E2 protein tetrahydrofuran derivative HPV11 E1 protein
(1RK6) (1R6N) (1TUE) (1R6N)
Interleukin 2 diphenyl derivative IL2-Receptor
(1M47) (1M48) (1Z92)
HIV-1 Integrase chlorophenyl-dihydroquinolin acetic acid LEDGF
(3L3U) (3LPT) (2B4J)
TNFa subunit A chromen-4-one derivative TNFa subunit B
(1TNF) (2AZ5) (1TNF)
TNF receptor 1a thiazolidin-4-one derivative TNF-beta
(1EXT) (1FT4) (1TNR)
MDM4 subunit A chlorobenzyl-phenyl-imidazol derivative p53
(3DAB) (3LBJ) (3DAB)
  1. Structures used in comparative analyses (detailed in Tables 1 and 2) are taken from the 2P2I database of protein-protein complexes with known inhibitors of the protein-protein interaction. In each case, an ensemble is generated from the apo structure, pockets from this ensemble are analysed and compared with binding sites/interfaces determined from the inhibitor and protein-protein complex structures. In the case of TNF-alpha, the inhibitor disrupts a protein-protein interface in the native trimer, and the apo and protein-protein complex structure files are consequently the same