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 |
|---|---|---|---|
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.663 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.653 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.637 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.624 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.582 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.580 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.561 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.546 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.545 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.534 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.533 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.529 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.526 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.525 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.521 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.519 | |
| 1iy8 | NAD | Levodione reductase | / | 0.510 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.510 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.505 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.504 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.503 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.502 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.502 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.501 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.499 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.498 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.497 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.496 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.495 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.494 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.494 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.493 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.493 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.492 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.491 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.491 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.491 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.488 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.488 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.486 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.486 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.485 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.484 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.483 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.482 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.481 | |
| 4qec | NAP | ElxO | / | 0.481 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.480 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.480 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.480 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.480 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.480 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.480 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.479 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.479 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.479 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.476 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.476 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.476 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.475 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.475 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.473 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.473 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.471 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.470 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.470 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.470 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.469 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.468 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.467 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.467 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.466 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.466 | |
| 4qed | NAP | ElxO | / | 0.466 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.463 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.463 | |
| 3uce | NDP | Dehydrogenase | / | 0.462 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.462 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.461 | |
| 1sny | NAP | LD36273p | / | 0.460 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.460 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.460 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.459 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.458 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.458 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.458 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.457 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.456 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.456 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.456 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.454 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.453 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.450 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.450 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.449 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.448 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.448 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.448 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.448 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.448 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.446 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.446 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.446 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.445 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.445 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.443 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.442 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.441 |