sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.676 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.662 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.661 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.647 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.628 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.627 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.605 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.605 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.595 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.563 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.562 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.551 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.551 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.481 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.478 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.476 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.473 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.472 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.472 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.472 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.466 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.464 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.463 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.463 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.462 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.461 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.461 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.460 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.459 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.459 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.459 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.457 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.456 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.455 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.455 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.454 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.450 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.450 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.450 | |
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.449 | |
| 3c21 | 2BA | DNA integrity scanning protein DisA | / | 0.449 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.448 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.448 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.447 | |
| 3a1c | ACP | Probable copper-exporting P-type ATPase A | 3.6.3.54 | 0.447 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.447 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.446 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 4i9n | 1E5 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.446 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.446 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.445 | |
| 2e15 | SAH | Diphthine synthase | / | 0.445 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.445 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.445 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.444 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.444 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.444 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.443 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.442 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.442 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.441 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.441 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.441 | |
| 4hdh | ATP | Genome polyprotein | 2.7.7.48 | 0.441 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.440 |