sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1gvr | TNL | Pentaerythritol tetranitrate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1gvr | TNL | Pentaerythritol tetranitrate reductase | / | 1.000 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.703 | |
| 1h62 | ANB | Pentaerythritol tetranitrate reductase | / | 0.625 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.624 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.548 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.537 | |
| 1h61 | PDN | Pentaerythritol tetranitrate reductase | / | 0.534 | |
| 3p80 | P80 | Pentaerythritol tetranitrate reductase | / | 0.530 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.529 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.519 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.512 | |
| 2gs9 | SAH | Uncharacterized protein | / | 0.508 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.505 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.501 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.501 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.487 | |
| 4f0r | MTA | 5-methylthioadenosine/S-adenosylhomocysteine deaminase | / | 0.480 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.476 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.473 | |
| 3kft | NAD | Pentaerythritol tetranitrate reductase | / | 0.472 | |
| 2cek | N8T | Acetylcholinesterase | 3.1.1.7 | 0.471 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 1zgb | A1E | Acetylcholinesterase | 3.1.1.7 | 0.470 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.470 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.469 | |
| 2ct8 | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.467 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.465 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.465 | |
| 4ara | C56 | Acetylcholinesterase | 3.1.1.7 | 0.464 | |
| 1eve | E20 | Acetylcholinesterase | 3.1.1.7 | 0.462 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.461 | |
| 3dy8 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.461 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.461 | |
| 2j3q | TFL | Acetylcholinesterase | 3.1.1.7 | 0.460 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1odc | A8B | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 1xh7 | R96 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.459 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 4kq6 | DLZ | 6,7-dimethyl-8-ribityllumazine synthase | / | 0.459 | |
| 4b7z | Q4Q | Acetylcholinesterase | 3.1.1.7 | 0.458 | |
| 3t4e | NAD | Quinate/shikimate dehydrogenase | / | 0.457 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 4ey7 | E20 | Acetylcholinesterase | 3.1.1.7 | 0.456 | |
| 1k4m | NAD | Nicotinate-nucleotide adenylyltransferase | 2.7.7.18 | 0.455 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.455 | |
| 2w6c | BM4 | Acetylcholinesterase | 3.1.1.7 | 0.455 | |
| 2xui | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 3h3q | H13 | Collagen type IV alpha-3-binding protein | / | 0.454 | |
| 2qim | ZEA | Class 10 plant pathogenesis-related protein | / | 0.453 | |
| 2xup | TZ5 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 4g2j | 0WF | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.453 | |
| 2ea2 | F77 | Methionine aminopeptidase 2 | / | 0.452 | |
| 3uzz | ASD | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.452 | |
| 1dx6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.451 | |
| 3qgf | 46F | Genome polyprotein | 2.7.7.48 | 0.451 | |
| 4lh7 | 1X8 | DNA ligase | / | 0.451 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.450 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1vi2 | NAD | Quinate/shikimate dehydrogenase | / | 0.450 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.450 | |
| 4arb | C57 | Acetylcholinesterase | 3.1.1.7 | 0.450 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.449 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 2ha6 | SCK | Acetylcholinesterase | 3.1.1.7 | 0.448 | |
| 3c89 | ARG_ARG_GLY_MET_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.448 | |
| 3qw8 | CYS_ARG_GLY_CYS_NH2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.448 | |
| 4qen | SAH | Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4 | 2.1.1.43 | 0.448 | |
| 1y1r | ANU | Uridine phosphorylase | 2.4.2.3 | 0.447 | |
| 2ga2 | A19 | Methionine aminopeptidase 2 | / | 0.447 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 3dyq | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 1kh3 | ANP | Argininosuccinate synthase | / | 0.446 | |
| 1pz0 | NAP | Protein IolS | 1.1.1 | 0.446 | |
| 1w76 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1yda | AZM | Carbonic anhydrase 2 | 4.2.1.1 | 0.446 | |
| 2xuo | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.446 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1w6r | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1ygk | RRC | Pyridoxal kinase | 2.7.1.35 | 0.445 | |
| 1zji | 2PG | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.445 | |
| 2cft | PLP | Pyridoxal phosphate phosphatase | / | 0.445 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.445 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.445 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.445 | |
| 1gky | 5GP | Guanylate kinase | 2.7.4.8 | 0.444 | |
| 1h6c | NDP | Glucose--fructose oxidoreductase | 1.1.99.28 | 0.444 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.444 | |
| 2pj4 | 414 | Carboxypeptidase B | / | 0.444 | |
| 3jyq | NAD | Quinate/shikimate dehydrogenase (NAD(+)) | / | 0.444 | |
| 4diq | PD2 | Ribosomal oxygenase 1 | / | 0.444 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.443 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.443 | |
| 1wbs | LI2 | Mitogen-activated protein kinase 14 | / | 0.443 | |
| 2ckm | AA7 | Acetylcholinesterase | 3.1.1.7 | 0.443 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.443 | |
| 2yy2 | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 3g1r | FIT | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.443 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.443 | |
| 4fxy | 0W2 | Neurolysin, mitochondrial | 3.4.24.16 | 0.443 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.442 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 3dys | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4ef4 | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 1mxf | MTX | Putative pteridine reductase 2 | / | 0.441 | |
| 1u65 | CP0 | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2pk3 | A2R | GDP-6-deoxy-D-mannose reductase | / | 0.441 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.441 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.441 | |
| 4dpt | AGS | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.440 | |
| 1ni4 | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.440 | |
| 2zr9 | DTP | Protein RecA | / | 0.440 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3g72 | A6T | Renin | 3.4.23.15 | 0.440 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.440 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 3nt5 | NAI | Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase | 1.1.1.18 | 0.440 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.440 | |
| 4ijr | NDP | D-arabinose dehydrogenase [NAD(P)+] heavy chain | 1.1.1.117 | 0.440 |