A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)
Fig 11
Alignments of high-scoring binding site pairs of the Barelier data set generated by (A) Cavbase, (B) TM-align, (C) SMAP, and (D) Shaper. (A) Superposition of angiotensin-converting enzyme (PDB ID 2x8z, green) and leukotriene A4 hydrolase (PDB ID 4dpr, purple) in complex with captopril (ball-and-sticks representation). Red spheres denote hydrogen bond acceptor features while purple spheres represent mixed hydrogen bond acceptor/donor features. Metal coordination sites are marked by orange spheres and blue and yellow spheres denote residues with aromatic and aliphatic characteristics, respectively. The Cavbase similarity score for this match is 11.37. (B) Alignment of leukotriene A4 hydrolase (PDB ID 3fty, green) and mitogen-activated protein kinase 14 (PDB ID 1w7h, purple) crystallized with the small molecule fragment 3-(benzyloxy)-pyridine-2-amine (3IP, ball-and-sticks-representation). Residues within a 4 Å radius of any ligand atom are depicted in stick representation. This alignment yields a TM-score of 0.32. (C) Superposition of adipocyte lipid-binding protein (PDB ID 2ans, green) and pheromone-binding protein (PDB ID 1ow4, purple) in complex with the fluorescent probe 8-anilino-1-naphthalene sulfonate (2AN, ball-and-sticks). The residues shown in stick representation represent only a fraction of all matched residues. The SMAP RawScore for this site pair is 63.44. (D) Shaper-based alignment of the neocarzinostatin (PDB ID 2g0l, green) and tankyrase-2 (PDB ID 4hki, purple) flavone (FLN, ball-and-sticks) binding sites (TanimotoCombo = 0.92). Residues within a 4 Å radius of the ligand are represented as sticks. Hydrogen bond interactions are depicted as green springs.