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.

A Santos et al.

A Santos et al. BMC Bioinformatics 2012 13:162   doi:10.1186/1471-2105-13-162

Open Data