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 |
|---|---|---|---|
| 3kb6 | NAD | D-lactate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3kb6 | NAD | D-lactate dehydrogenase | / | 1.000 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.522 | |
| 2gcg | NDP | Glyoxylate reductase/hydroxypyruvate reductase | 1.1.1.79 | 0.508 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.488 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.488 | |
| 2dbz | NAP | Glyoxylate reductase | 1.1.1.26 | 0.484 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.483 | |
| 4e5k | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.481 | |
| 1nzd | UPG | DNA beta-glucosyltransferase | / | 0.479 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.476 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.475 | |
| 2eud | GCQ | Ribonucleoside-diphosphate reductase large chain 1 | 1.17.4.1 | 0.475 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.473 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.473 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.473 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.473 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.472 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.471 | |
| 2dbq | NAP | Glyoxylate reductase | 1.1.1.26 | 0.471 | |
| 3baz | NAP | Hydroxyphenylpyruvate reductase | 1.1.1.237 | 0.471 | |
| 1hku | NAD | C-terminal-binding protein 1 | 1.1.1 | 0.470 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.466 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.466 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.465 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.465 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.465 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 2w2l | NAD | D-mandelate dehydrogenase | / | 0.464 | |
| 2x0i | NAI | Malate dehydrogenase | / | 0.463 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.463 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.462 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.462 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.460 | |
| 4xfj | ANP | Argininosuccinate synthase | / | 0.460 | |
| 5j23 | A2R | Putative 2-hydroxyacid dehydrogenase | / | 0.460 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.459 | |
| 4weq | NAP | NAD-dependent dehydrogenase | / | 0.459 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.458 | |
| 3fri | SAH | 16S rRNA methylase | / | 0.458 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.458 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.458 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 2g76 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.457 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.457 | |
| 4bft | ZVT | Pantothenate kinase | 2.7.1.33 | 0.457 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.457 | |
| 4nu5 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.457 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4bj9 | UHB | Tankyrase-2 | 2.4.2.30 | 0.456 | |
| 4itf | TFY | Vitamin D3 receptor | / | 0.456 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.455 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.455 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.454 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.454 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.454 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.454 | |
| 2ekl | NAD | D-3-phosphoglycerate dehydrogenase | / | 0.454 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.454 | |
| 3crl | ANP | [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial | 2.7.11.2 | 0.454 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1nzf | UPG | DNA beta-glucosyltransferase | / | 0.453 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.453 | |
| 3dhe | AND | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.453 | |
| 3kbo | NDP | Glyoxylate/hydroxypyruvate reductase A | / | 0.453 | |
| 1dbv | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.452 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.452 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.452 | |
| 4z0p | NDP | NAD-dependent dehydrogenase | / | 0.452 | |
| 1dgm | ADN | Adenosine kinase | 2.7.1.20 | 0.451 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.451 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.451 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.451 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1rbz | KT5 | Trifunctional purine biosynthetic protein adenosine-3 | 2.1.2.2 | 0.450 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.450 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.450 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.450 | |
| 3fwj | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3wrm | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.450 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4njo | NAD | D-3-phosphoglycerate dehydrogenase, putative | / | 0.450 | |
| 4nu6 | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.450 | |
| 1dz6 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.449 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.449 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.449 | |
| 2qn3 | F55 | Glycogen phosphorylase, muscle form | 2.4.1.1 | 0.449 | |
| 2y3r | TRK | TamL | / | 0.449 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 3o6o | 94M | Heat shock protein 83 | / | 0.449 | |
| 3t4n | ADP | 5'-AMP-activated protein kinase subunit gamma | / | 0.449 | |
| 3zw9 | NAD | Peroxisomal bifunctional enzyme | 1.1.1.35 | 0.449 | |
| 4e5m | NAP | Phosphonate dehydrogenase | 1.20.1.1 | 0.449 | |
| 1drh | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 2ejz | SAH | Diphthine synthase | / | 0.448 | |
| 3t3r | 9PL | Cytochrome P450 2A6 | 1.14.13 | 0.448 | |
| 2hu2 | NAD | C-terminal binding protein 1 | / | 0.447 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 2y05 | NAP | Prostaglandin reductase 1 | / | 0.447 | |
| 2yvw | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.447 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 4z17 | PEP | Enolase | / | 0.447 | |
| 5a3b | APR | SIR2 family protein | / | 0.447 | |
| 1a9z | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.446 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.446 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.446 | |
| 2xh9 | J01 | Uncharacterized protein | / | 0.446 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.446 | |
| 4l4e | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.446 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.446 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3nr4 | PYV | Abscisic acid receptor PYL2 | / | 0.445 | |
| 3vt7 | VDX | Vitamin D3 receptor | / | 0.445 | |
| 4yxm | 2BA | DNA integrity scanning protein DisA | / | 0.445 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.444 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 2dra | ATP | CCA-adding enzyme | 2.7.7.72 | 0.444 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.444 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.444 | |
| 3uth | FDA | UDP-galactopyranose mutase | / | 0.444 | |
| 4n9w | GDP | Phosphatidyl-myo-inositol mannosyltransferase | 2.4.1.57 | 0.444 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.444 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.443 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.443 | |
| 2zh6 | ATP | CCA-adding enzyme | 2.7.7.72 | 0.443 | |
| 4blr | UTP | NTPase P4 | / | 0.443 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.443 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.443 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.443 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.442 | |
| 1wwk | NAD | 307aa long hypothetical phosphoglycerate dehydrogenase | / | 0.442 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.442 | |
| 2eka | SAH | Diphthine synthase | / | 0.442 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.442 | |
| 2yww | ATP | Aspartate carbamoyltransferase regulatory chain | / | 0.442 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.442 | |
| 4ge4 | 0KE | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.442 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.442 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2qbl | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial | 1.2.4.1 | 0.441 | |
| 3exh | TPP | Pyruvate dehydrogenase E1 component subunit beta, mitochondrial | 1.2.4.1 | 0.441 | |
| 3gob | HXX | DdmC | / | 0.441 | |
| 3h6v | NS6 | Glutamate receptor 2 | / | 0.441 | |
| 4pnm | NU1 | Tankyrase-2 | 2.4.2.30 | 0.441 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.440 | |
| 1gzu | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.440 | |
| 1u2y | GOX | Pancreatic alpha-amylase | / | 0.440 | |
| 1yrd | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.440 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.440 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.440 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.440 | |
| 3utg | FDA | UDP-galactopyranose mutase | / | 0.440 | |
| 4e5n | NAD | Phosphonate dehydrogenase | 1.20.1.1 | 0.440 | |
| 4ien | COA | Putative acyl-CoA hydrolase | / | 0.440 | |
| 5a3c | NAD | SIR2 family protein | / | 0.440 | |
| 5dp2 | NAP | CurF | / | 0.440 |