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 |
|---|---|---|---|
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.686 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.631 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.623 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.621 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.615 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.610 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.594 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.567 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.564 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.550 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.548 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.542 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.532 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.526 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.526 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.526 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.526 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.525 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.524 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.521 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.519 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.518 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.518 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.517 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.516 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.516 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.516 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.514 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.514 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.513 | |
| 1iy8 | NAD | Levodione reductase | / | 0.512 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.511 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.508 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.507 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.505 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.503 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.503 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.502 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.501 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.500 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.499 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.499 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.498 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.498 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.498 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.497 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.495 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.494 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.494 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.491 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.491 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.490 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.490 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.489 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.489 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.489 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.487 | |
| 1sny | NAP | LD36273p | / | 0.486 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.485 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.485 | |
| 4qec | NAP | ElxO | / | 0.485 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.484 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.483 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.482 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.482 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.481 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.480 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.480 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.480 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.479 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.478 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.477 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.477 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.477 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.477 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.476 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.476 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.476 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.476 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.475 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.473 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.473 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.469 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.469 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.467 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.467 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.467 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.466 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.464 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.464 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.464 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.463 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.463 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.463 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.462 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.461 | |
| 4qed | NAP | ElxO | / | 0.460 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.458 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.458 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.457 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.456 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.456 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.456 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.455 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.455 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.454 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.453 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.452 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.452 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.451 | |
| 4g3j | VNT | Lanosterol 14-alpha-demethylase | / | 0.451 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.450 | |
| 3bmo | NAP | Pteridine reductase | / | 0.449 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.445 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 |