A new protein binding pocket similarity measure based on comparison of clouds of atoms in 3D: application to ligand prediction

Table 2 Ligands descriptors for the homogeneous dataset

ligand	Atom count	Molecular weight	hydrogen-bond acceptors	hydrogen-bond donors	Rotatable bonds
PMP	16	247.17	4	4	4
SUC	23	342.3	11	8	5
LLP	24	361.33	5	6	11
LDA	16	229.4	1	0	11
BOG	20	292.37	6	4	9
PLM	18	255.42	2	0	14
SAM	27	399.45	8	7	7
U5P	21	322.17	8	3	4
GSH	20	306.32	6	6	11
1PE	14	208.25	5	1	11
Average	19.9 ± 4.0	296.4 ± 61.5	5.6 ± 3.0	3.9 ± 2.9	8.7 ± 3.5

PMP: 4'-deoxy-4'-aminopyridoxal-5'-phosphate, SUC: sucrose, LLP: 2-lysine(3-hydroxy-2-methyl-5-phosphonooxymethyl- pyridin-4-ylmethane), LDA: lauryl dimethylamine-N-oxide, BOG: b-octylglucoside, PLM: palmitic acid, SAM: S-adenosylmethionine, U5P: uridine-5'-monophosphate, GSH: glutathione, 1PE: pentaethylene glycol.

ISSN: 1471-2105