Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study

Table 2 Protein binding-sites that bind non-hexose ligands

PDB ID	Cavity center	Ligand	PDB ID	Cavity center	Ligand
Hexose-like ligands
1A8U	4320, 4323	BEZ-1	1AI7	6074, 6077	IPH-1
1AWB	4175, 4178	IPD-2	1DBN	pyranose ring	GAL-102
1EOB	3532, 3536	DHB-999	1F9G	5792, 5785, 5786	ASC-950
1G0H	4045, 4048	IPD-292	1JU4	4356, 4359	BEZ-1
1LBX	3941, 3944	IPD-295	1LBY	3944, 3939, 3941	F6P-295
1LIU	15441, 15436, 15438	FBP-580	1MOR	pyranose ring	G6P-609
1NCW	3406, 3409	BEZ-601	1P5D	pyranose ring	G1P-658
1T10	4366, 4361, 4363	F6P-1001	1U0F	pyranose ring	G6P-900
1UKB	2144, 2147	BEZ-1300	1X9I	pyranose ring	G6Q-600
1Y9G	4124, 4116, 4117	FRU-801	2B0C	pyranose ring	G1P-496
2B32	3941, 3944	IPH-401	4PBG	pyranose ring	BGP-469
Other ligands
11AS	5132	ASN-1	11GS	1672, 1675	MES-3
1A0J	6985	BEN-246	1A42	2054, 2055	BZO-555
1A50	4939, 4940	FIP-270	1A53	2016, 2017	IGP-300
1AA1	4472, 4474	3PG-477	1AJN	6074, 6079	AAN-1
1AJS	3276, 3281	PLA-415	1AL8	2652	FMN-360
1B8A	7224	ATP-500	1BO5	7811	GOL-601
1BOB	2566	ACO-400	1D09	7246	PAL-1311
1EQY	3831	ATP-380	1IOL	2674, 2675	EST-400
1JTV	2136, 2137	TES-500	1KF6	16674, 16675	OAA-702
1RTK	3787, 3784	GBS-300	1TJ4	1947	SUC-1
1TVO	2857	FRZ-1001	1UK6	2142	PPI-1300
1W8N	4573, 4585	DAN-1649	1ZYU	1284, 1286	SKM-401
2D7S	3787	GLU-1008	2GAM	11955	NGA-502
3PCB	3421, 3424	3HB-550

The table lists the protein’s PDB ID, the ligand considered and the specified cavity center. 22 ligands are similar to hexoses in shape and/or size. The cavity center is the centroid of the reported PDB atom numbers.

ISSN: 1471-2105