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 |
|---|---|---|---|
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3hyg | 099 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 1.000 | |
| 3hy7 | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.670 | |
| 3ljt | LA3 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.642 | |
| 3hy9 | 098 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.631 | |
| 3b8z | 294 | A disintegrin and metalloproteinase with thrombospondin motifs 5 | 3.4.24 | 0.617 | |
| 2jih | 097 | A disintegrin and metalloproteinase with thrombospondin motifs 1 | 3.4.24 | 0.490 | |
| 4dd8 | BAT | Disintegrin and metalloproteinase domain-containing protein 8 | 3.4.24 | 0.479 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.478 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.474 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.471 | |
| 5dp2 | NAP | CurF | / | 0.471 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.467 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.465 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.465 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.465 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.463 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.460 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.456 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.456 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.455 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.455 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.454 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.454 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.454 | |
| 2z7h | GG3 | Geranylgeranyl pyrophosphate synthase | / | 0.454 | |
| 3ens | ENS | Coagulation factor X | 3.4.21.6 | 0.454 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.453 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.452 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.452 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.452 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.452 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4hbm | 0Y7 | E3 ubiquitin-protein ligase Mdm2 | 6.3.2 | 0.452 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.451 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.451 | |
| 1ja0 | FMN | NADPH--cytochrome P450 reductase | / | 0.450 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.449 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.448 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.447 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.447 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.447 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.446 | |
| 5cfl | C2E | Stimulator of interferon genes protein | / | 0.446 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.445 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.445 | |
| 3lgp | 50X | Disintegrin and metalloproteinase domain-containing protein 17 | 3.4.24.86 | 0.445 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.445 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.445 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3u9f | CLM | Chloramphenicol acetyltransferase | 2.3.1.28 | 0.444 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.443 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.443 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.443 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.443 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.443 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.442 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.442 | |
| 3ivx | FG6 | Pantothenate synthetase | 6.3.2.1 | 0.442 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.442 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.441 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.441 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.441 | |
| 3nut | SAH | Precorrin-3 methylase | / | 0.441 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.441 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.441 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.440 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.440 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 5a4v | QUE | Glutathione S-transferase F2 | 2.5.1.18 | 0.440 |