Examples of small molecule binding at the interface of Pfam-A domains. (a) Binding of thiorphan at the active site of thermolysin. The phenyl ring binds within the S1' pocket, the sulfur atom is coordinated with the active site Zinc atom (not shown). Thiorphan binds residues of both, the thermolysin metalloprotease catalytic domain (Peptidase_M4, red) and C-terminal domain (Peptidase_M4_C, green). (b) Nocodazole binding to the prostaglandin/GSH site of the human haematopoetic prostaglandin synthase D2. Nocodazole binds at the interface between the glutathione S-transferase N-terminal (GST_N, green) and C-terminal (GST_C, red) domains. (c) Etoposide binding to the DNA cleavage site of human type II DNA topoisomerase. The ligand binds residues both of the Toprim domain (green) and DNA topoisomerase IV domain (DNA_topoisoIV, red). (d) Nicotinamide-adenine dinucleotide binding to the active site of human alcohol dehydrogenase beta-1-beta-1 isoform. Binding takes place at the interface of the Alcohol dehydrogenase GroES-like domain (ADH_N, green) and Zinc-binding dehydrogenase domain (ADH_ZINC_N, red). Examples were rendered using PDB files 1zdp, 3ee2, 3qx3, 1u3u, respectively.
Kruger et al. BMC Bioinformatics 2012 13(Suppl 17):S11 doi:10.1186/1471-2105-13-S17-S11