. Author manuscript; available in PMC: 2013 Apr 1.

Published in final edited form as: Proteins. 2012 Jan 24;80(4):1177–1195. doi: 10.1002/prot.24018

Table 1A.

The ligand pocket benchmark dataset from Kahraman et al.

Binding ligand molecule	Average Size^a) (Å)	Molecular mass (g/mol)	Average number of seeds^b)	Number of PDB entries	PDB entries
AMP	8.8	347.22	23.7	9	12asA, 1amuA, 1c0aA, 1ct9A, 1jp4A, 1khtB, 1qb8A, 1tb7B, 8gpbA
ATP	9.5	507.18	29.5	14	1a0iA, 1a49A, 1aylA, 1b8aA, 1dv2A, 1dy3A, 1e2qA, 1e8xA, 1esqA, 1gn8B, 1kvkA, 1o9tA, 1rdqE, 1tidA
FAD	11	785.55	44.1	10	1cqxA, 1e8gB, 1eviB, 1h69A, 1hskA, 1jqiA, 1jr8B, 1k87A, 1poxA, 3grsA
FMN	9.7	456.34	27.7	6	1dnlA, 1f6vA, 1ja1A, 1mvlA, 1p4cA, 1p4mA
GLC	8.5	180.16	15.2	5	1bdgA, 1cq1A, 1k1wA, 1nf5C, 2gbpA
HEM	10.2	616.49	36.9	16	1d0cA, 1d7cA, 1dk0A, 1eqgA, 1ew0A, 1gweA, 1iqcA, 1nazE, 1np4B, 1po5A, 1pp9C, 1qhuA, 1qlaC, 1qpaB, 1soxA, 2cpoA
NAD	10.1	663.43	36.8	15	1ej2B, 1hexA, 1ib0A, 1jq5A, 1mewA, 1mi3A, 1o04A, 1og3A, 1qaxA, 1rlzA, 1s7gB, 1t2dA, 1toxA, 2a5fB, 2npxA
PO4	7.4	94.97	9.7	20	1a6q, 1b8oC, 1brwA, 1cqjB, 1d1qB, 1dakA, 1e9gA, 1ejdC, 1eucA, 1ew2A, 1fbtB, 1gypA, 1h6lA, 1ho5B, 1l5wA, 1l7mA, 1lbyA, 1lyvA, 1qf5A, 1tcoA
STR	9.2	278.8	22.2	5	1e3rB, 1fdsA, 1j99A, 1lhuA, 1qktA

^a)

The pocket size is defined as the average distance from the center of the mass of the pocket to the pocket surface.

^b)

The average number of seed points in the pockets.