PubChem3D: Biologically relevant 3-D similarity

Table 1 Summary statistics of chemical structure descriptors.

	Biologically Tested Compounds (734,486 CIDs)	Entire PubChem3D Contents (26,157,365 CIDs)
Heavy atom count	24.6 ± 6.4	26.3 ± 7.0
Monopole volume (Å³)	474.1 ± 124.0	509.0 ± 137.1
Q_x (Å⁵)	12.6 ± 7.0	13.6 ± 7.8
Q_y (Å⁵)	3.3 ± 1.6	3.6 ± 1.8
Q_z (Å⁵)	1.3 ± 0.6	1.5 ± 0.6
Total feature count	8.1 ± 2.6	8.5 ± 2.7
Hydrogen-bond acceptor count	2.9 ± 1.6	3.0 ± 1.6
Hydrogen-bond donor count	1.1 ± 1.0	1.2 ± 1.0
Anion count	0.2 ± 0.4	0.2 ± 0.4
Cation count	0.6 ± 0.8	0.7 ± 0.9
Hydrophobe count	0.3 ± 0.6	0.5 ± 0.8
Ring count	3.0 ± 1.2	3.0 ± 1.3

The average and standard deviation of heavy atom count, monopole volume, quadrupole components, and feature counts (by total and each of the six feature types) for 734,486 CIDs biologically tested compounds considered in this study and those for the entire PubChem3D contents (26,157,365 CIDs as of September 2010).

ISSN: 1758-2946