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 |
|---|---|---|---|
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1cbf | SAH | Cobalt-precorrin-4 C(11)-methyltransferase | 2.1.1.271 | 1.000 | |
| 3ndc | SAH | Precorrin-4 C(11)-methyltransferase | 2.1.1.133 | 0.558 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.476 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.473 | |
| 1v9a | SAH | Uncharacterized protein | / | 0.472 | |
| 2e07 | SAH | Diphthine synthase | / | 0.471 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.471 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.470 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.469 | |
| 2huq | SAH | Diphthine synthase | / | 0.467 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.467 | |
| 1vsv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.466 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.466 | |
| 2ejj | SAH | Diphthine synthase | / | 0.465 | |
| 2p5c | SAH | Diphthine synthase | / | 0.465 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.464 | |
| 2y3r | TRK | TamL | / | 0.463 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.463 | |
| 2owu | SAH | Diphthine synthase | / | 0.461 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.460 | |
| 3iae | D7K | Benzaldehyde lyase | / | 0.460 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.460 | |
| 3pym | NAD | Glyceraldehyde-3-phosphate dehydrogenase 3 | 1.2.1.12 | 0.460 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.459 | |
| 2qbm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.459 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.459 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.459 | |
| 2cpp | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.458 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.458 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.458 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.458 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.457 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.457 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.457 | |
| 2dv7 | SAH | Diphthine synthase | / | 0.457 | |
| 2ev9 | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.457 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.457 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.456 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.456 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.456 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.455 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.455 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.454 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1wng | SAH | Diphthine synthase | / | 0.454 | |
| 2ed5 | SAH | Diphthine synthase | / | 0.454 | |
| 3dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.454 | |
| 4kne | 1CY | Dihydrofolate reductase | 1.5.1.3 | 0.454 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.454 | |
| 2e8q | SAH | Diphthine synthase | / | 0.453 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.453 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.452 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.452 | |
| 2dv5 | SAH | Diphthine synthase | / | 0.452 | |
| 2en5 | SAH | Diphthine synthase | / | 0.452 | |
| 3ieu | GDP | GTPase Era | / | 0.452 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.452 | |
| 2e16 | SAH | Diphthine synthase | / | 0.451 | |
| 2p5f | SAH | Diphthine synthase | / | 0.451 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.451 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.451 | |
| 3wrl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.450 | |
| 2p2x | SAH | Diphthine synthase | / | 0.450 | |
| 1mkd | ZAR | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.449 | |
| 1phg | MYT | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.449 | |
| 2z6r | SAH | Diphthine synthase | / | 0.449 | |
| 1x27 | ASP_TYR_VAL_HIS_PTR | Tyrosine-protein kinase Lck | 2.7.10.2 | 0.448 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.448 | |
| 2dek | SAH | Diphthine synthase | / | 0.448 | |
| 2e08 | SAH | Diphthine synthase | / | 0.448 | |
| 2e17 | SAH | Diphthine synthase | / | 0.448 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.448 | |
| 3wv7 | ADP | Hmd co-occurring protein HcgE | / | 0.448 | |
| 5cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.448 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1iwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 1tdr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2dsh | SAH | Diphthine synthase | / | 0.447 | |
| 2dxv | SAH | Diphthine synthase | / | 0.447 | |
| 2dxw | SAH | Diphthine synthase | / | 0.447 | |
| 2q9f | C3S | Cholesterol 24-hydroxylase | / | 0.447 | |
| 3drc | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.447 | |
| 3eks | CY9 | Actin-5C | / | 0.447 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.447 | |
| 3r6s | CMP | CRP-like cAMP-activated global transcriptional regulator | / | 0.447 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.446 | |
| 2dbv | NDP | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 2hux | SAH | Diphthine synthase | / | 0.446 | |
| 2p6i | SAH | Diphthine synthase | / | 0.446 | |
| 2pb4 | SAH | Diphthine synthase | / | 0.446 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.446 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.446 | |
| 3csd | EMO | Putative ketoacyl reductase | 1.3.1 | 0.446 | |
| 4jx1 | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.445 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.445 | |
| 1kt8 | ILP | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.445 | |
| 2emu | SAH | Diphthine synthase | / | 0.445 | |
| 2y4g | TIR | TamL | / | 0.445 | |
| 3a3g | DLZ | Lumazine protein | / | 0.445 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.445 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 4rvn | COA | Phenylacetate-coenzyme A ligase | / | 0.445 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.444 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.444 | |
| 2vke | TAC | Tetracycline repressor protein class D | / | 0.444 | |
| 3eko | PYU | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.444 | |
| 4h6p | FMN | Chromate reductase | / | 0.444 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.444 | |
| 2o7o | DXT | Tetracycline repressor protein class D | / | 0.443 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4aox | FAD | Steroid monooxygenase | / | 0.443 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.442 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.442 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 2hr8 | SAH | Diphthine synthase | / | 0.442 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.442 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.442 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3iqh | TYR_ASP_ILE | Cysteine synthase | 2.5.1.47 | 0.442 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.442 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.442 | |
| 4emt | C2E | Stimulator of interferon genes protein | / | 0.442 | |
| 4xcv | NDP | Probable hydroxyacid dehydrogenase protein | / | 0.442 | |
| 4z0h | NAD | Glyceraldehyde-3-phosphate dehydrogenase GAPC1, cytosolic | 1.2.1.12 | 0.442 | |
| 5a9s | NAP | Putative dehydrogenase | / | 0.442 | |
| 1dyj | DDF | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 2a1n | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2ath | 3EA | Peroxisome proliferator-activated receptor gamma | / | 0.441 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.441 | |
| 2nni | MTK | Cytochrome P450 2C8 | / | 0.441 | |
| 2qd3 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.441 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 4enh | FVX | Cholesterol 24-hydroxylase | / | 0.441 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.441 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.440 | |
| 1noo | CAH | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2egl | SAH | Diphthine synthase | / | 0.440 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.440 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.440 | |
| 3p0j | TYE | Putative tyrosyl-tRNA synthetase | / | 0.440 | |
| 4l4f | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.440 |