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 |
|---|---|---|---|
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.665 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.650 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.644 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.625 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.621 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.615 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.559 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.557 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.550 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.544 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.527 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.526 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.523 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.522 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.520 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.519 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.516 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.509 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.507 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.504 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.504 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.504 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.504 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.503 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.502 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.501 | |
| 1iy8 | NAD | Levodione reductase | / | 0.500 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.500 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.500 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.499 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.498 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.495 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.495 | |
| 4qec | NAP | ElxO | / | 0.493 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.492 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.492 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.490 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.490 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.490 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.489 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.488 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.487 | |
| 3sju | NDP | Keto reductase | / | 0.486 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.486 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.486 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.485 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.484 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.484 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.484 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.484 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.484 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.483 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.483 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.483 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.483 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.482 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.480 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.480 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.480 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.480 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.480 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.480 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.479 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.479 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.477 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.477 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.476 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.475 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.475 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.475 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.474 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.474 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.473 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.473 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.472 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.471 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.471 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.469 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.465 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.464 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.463 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.463 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.463 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.462 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.460 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.459 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.459 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.459 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.457 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.457 | |
| 1sny | NAP | LD36273p | / | 0.456 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.456 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.453 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.453 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.452 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.450 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.450 | |
| 4qed | NAP | ElxO | / | 0.449 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.448 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.448 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.446 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.445 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.443 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.441 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.441 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 |