A simple method for finding a protein’s ligand-binding pockets

BMC Structural Biology

Table 3 Pockets and their characteristics recognized by our method for 1A6U protein atoms

Pocket Num.^*	Num. of Atoms	Num. of Empty voxels	Surface of Pocket	Depth of Pocket	NoA^**HA^aBonds	NoA HD^bBonds	NoA vdW^***Bonds	NoA Ionic Bonds	NoA Sulfur Bonds	NoA	cf	cf
										C-Ring	of the 1^stAS, HAP^c	of the 2^ndAS, AC1^c
1	63	401	116.25	28.40	5	8	0	1	0	20	0.31	0.33
5	80	481	21.83	38.66	2	3	10	2	0	2	0	0
18	101	648	187.27	25.83	5	7	6	2	0	14	0.12	0.11
19	67	411	84.36	19.35	1	2	5	0	0	2	0	0
38	44	266	138.90	20.63	1	4	1	0	0	6	0	0
39	85	499	82.58	28.26	3	5	2	0	0	14	0.31	0.22
40	21	127	77.97	14.53	2	3	0	0	0	4	0.06	0
58	118	765	340.90	29.83	5	4	7	3	0	3	0	0
59	86	529	253.20	26.72	4	4	4	2	0	6	0.06	0
85	226	1360	370.14	36.18	7	7	26	3	1	27	0	0
89	21	141	212.35	21.47	0	1	4	1	0	4	0	0
90	92	573	293.28	28.54	4	2	15	2	0	11	0	0
112	44	241	36.33	27.39	1	2	1	0	0	6	0.06	0
117	38	215	76.66	17.42	1	3	0	0	0	8	0	0
137	15	99	127.57	17.53	2	4	0	0	0	3	0.25	0.33
143	55	354	259.10	24.24	4	8	0	1	0	20	0.43	0.55

^*Pocket number indicates the number in the protein’s atomic positions convex hull surface rows, and they correspond to three vertices of triangles.
^**NoA means the number of atoms.
^***vdW means van der Waals.
^aHA means hydrogen bond acceptor.
^bHD means hydrogen bond donor.
^cThese are the cf-values (ratio of the number of correct residues to the total number of residues in the active site). For 1A6W in PDB two active sites (AS) are reported as HAP and AC1.

ISSN: 1472-6807