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 |
|---|---|---|---|
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.663 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.654 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.642 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.641 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.630 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.590 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.583 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.567 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.566 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.564 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.562 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.558 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.557 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.555 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.552 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.552 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.551 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.551 | |
| 1iy8 | NAD | Levodione reductase | / | 0.549 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.547 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.546 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.545 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.544 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.543 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.540 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.539 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.539 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.538 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.538 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.537 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.537 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.537 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.535 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.534 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.533 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.532 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.532 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.532 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.529 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.529 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.529 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.528 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.525 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.525 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.524 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.524 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.523 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.522 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.522 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.521 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.520 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.519 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.519 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.518 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.518 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.517 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.516 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.516 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.516 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.515 | |
| 1sny | NAP | LD36273p | / | 0.514 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.514 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.513 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.512 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.511 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.510 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.510 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.509 | |
| 4qec | NAP | ElxO | / | 0.509 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.508 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.508 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.507 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.506 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.506 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.505 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.504 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.504 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.503 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.501 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.500 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.499 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.497 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.497 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.497 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.494 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.494 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.494 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.494 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.493 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.492 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.488 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.488 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.488 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.487 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.486 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.486 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.485 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.484 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.483 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.483 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.480 | |
| 5dp2 | NAP | CurF | / | 0.479 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.475 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.473 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.473 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.471 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.470 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.469 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.468 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.467 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.467 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.467 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.467 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.467 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.466 | |
| 3uce | NDP | Dehydrogenase | / | 0.464 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.464 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.464 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.463 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.462 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.461 | |
| 4qed | NAP | ElxO | / | 0.461 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.460 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.459 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.457 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.457 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.455 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.455 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.454 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.453 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.453 | |
| 3bmo | NAP | Pteridine reductase | / | 0.452 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.452 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.451 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.451 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.450 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.448 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.448 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.448 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.448 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.447 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.446 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.446 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.444 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.441 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.441 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.440 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.440 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.440 |