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

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

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)

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