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 |
|---|---|---|---|
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 1.000 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.579 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.578 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.566 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.560 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.555 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.552 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.551 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.551 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.551 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.549 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.548 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.545 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.543 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.543 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.542 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.541 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.538 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.538 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.537 | |
| 1sny | NAP | LD36273p | / | 0.535 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.533 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.530 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.529 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.524 | |
| 4qec | NAP | ElxO | / | 0.523 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.522 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.522 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.521 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.521 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.521 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.520 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.519 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.519 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.519 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.518 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.518 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.516 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.515 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.514 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.514 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.513 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.513 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.512 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.510 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.510 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.510 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.508 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.508 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.508 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.507 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.507 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.506 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.505 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.504 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.504 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.504 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.503 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.502 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.500 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.499 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.498 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.498 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.498 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.498 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.496 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.496 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.496 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.495 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.495 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.494 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.493 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.493 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.491 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.491 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.491 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.490 | |
| 4wji | NAP | Putative cyclohexadienyl dehydrogenase and ADH prephenate dehydrogenase | / | 0.490 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.489 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.488 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.487 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.486 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.485 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.484 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.484 | |
| 2bfo | NDP | Pteridine reductase 1 | 1.5.1.33 | 0.483 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.483 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.483 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.482 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.481 | |
| 4qed | NAP | ElxO | / | 0.481 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.480 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.480 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.478 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.477 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 1hdo | NAP | Flavin reductase (NADPH) | / | 0.475 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.474 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.473 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.473 | |
| 1bdb | NAD | Cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase | / | 0.472 | |
| 3a3g | DLZ | Lumazine protein | / | 0.472 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.472 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.471 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.471 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.471 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.470 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.470 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.469 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.469 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.468 | |
| 3qwb | NDP | Probable quinone oxidoreductase | 1.6.5.5 | 0.468 | |
| 5dp2 | NAP | CurF | / | 0.468 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.466 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.466 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.465 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.465 | |
| 1iy8 | NAD | Levodione reductase | / | 0.464 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.463 | |
| 3bmo | NAP | Pteridine reductase | / | 0.463 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.461 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.461 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.460 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.460 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.459 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.459 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.458 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.457 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.457 | |
| 3sju | NDP | Keto reductase | / | 0.457 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.456 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.454 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.454 | |
| 3rkr | NAP | Uncharacterized protein | / | 0.453 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.453 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.452 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.452 | |
| 3hyo | ADP | Pyridoxal kinase | / | 0.451 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.450 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.450 | |
| 3kpb | SAM | Uncharacterized protein MJ0100 | / | 0.450 | |
| 2v6g | NAP | 3-oxo-Delta(4,5)-steroid 5-beta-reductase | / | 0.449 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.449 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.448 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.448 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.448 | |
| 4hp8 | NAP | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.448 | |
| 4j4n | D44 | Peptidylprolyl isomerase | / | 0.448 | |
| 1ju9 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.447 | |
| 2ex1 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.447 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.447 | |
| 3ieu | GDP | GTPase Era | / | 0.447 | |
| 3uce | NDP | Dehydrogenase | / | 0.447 | |
| 3zbr | NAP | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.447 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1n7g | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.446 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.446 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.446 | |
| 1kol | NAD | Glutathione-independent formaldehyde dehydrogenase | / | 0.445 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.445 | |
| 2cnt | COA | Ribosomal-protein-alanine acetyltransferase | / | 0.445 | |
| 3pw8 | ACO | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.445 | |
| 1fxs | NAP | GDP-L-fucose synthase | / | 0.444 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.443 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.443 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.443 | |
| 2ge3 | ACO | Probable acetyltransferase | / | 0.443 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.443 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.443 | |
| 3wie | DN4 | Glucose 1-dehydrogenase | / | 0.443 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.443 | |
| 1uay | ADN | Oxidoreductase | / | 0.442 | |
| 2yq9 | 2AM | 2',3'-cyclic-nucleotide 3'-phosphodiesterase | 3.1.4.37 | 0.442 | |
| 2fxv | 5GP | Xanthine phosphoribosyltransferase | 2.4.2.22 | 0.441 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.441 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.441 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 3b20 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.440 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 |