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 |
|---|---|---|---|
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 1.000 | |
| 2bjf | DXC | Choloylglycine hydrolase | 3.5.1.24 | 0.619 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.496 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.480 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.478 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.478 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.470 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.469 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.469 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.467 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.467 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.466 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.464 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.464 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.463 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.462 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.462 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.462 | |
| 4a87 | NAR | Major pollen allergen Bet v 1-A | / | 0.460 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.459 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.458 | |
| 4z61 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.458 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.457 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.456 | |
| 2y1t | DUD | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.456 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.455 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.455 | |
| 4kla | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.455 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.454 | |
| 1juv | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.453 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.453 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.453 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.453 | |
| 1kkq | 471 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.450 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.450 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.450 | |
| 3bk2 | U5P | Ribonuclease J | / | 0.450 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.450 | |
| 4jld | ADP | Adenylate kinase | / | 0.449 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.448 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.448 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.448 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.448 | |
| 1gpd | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.447 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.447 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.447 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.446 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.446 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.445 | |
| 1pjc | NAD | Alanine dehydrogenase | / | 0.445 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.445 | |
| 4yao | FMN | NADPH--cytochrome P450 reductase | / | 0.445 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.444 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.444 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.444 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.444 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.443 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.443 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.443 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.442 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.442 | |
| 4ike | ADP | Adenylate kinase | / | 0.442 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.442 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.441 | |
| 1rfu | ADP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.441 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.441 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.440 | |
| 2ejz | SAH | Diphthine synthase | / | 0.440 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.440 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.440 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.440 |