sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.681 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.660 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.642 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.623 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.621 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.612 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.592 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.559 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.557 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.554 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.552 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.547 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.546 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.546 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.546 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.544 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.542 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.542 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.540 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.540 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.540 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.537 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.537 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.537 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.535 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.534 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.533 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.532 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.531 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.530 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.530 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.530 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.529 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.529 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.528 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.528 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.528 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.528 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.528 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.527 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.527 | |
| 1iy8 | NAD | Levodione reductase | / | 0.526 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.526 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.526 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.525 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.525 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.524 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.524 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.522 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.521 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.521 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.520 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.518 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.517 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.515 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.515 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.515 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.514 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.514 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.514 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.513 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.513 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.513 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.511 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.511 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.509 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.508 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.507 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.506 | |
| 3bmo | NAP | Pteridine reductase | / | 0.505 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.504 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.503 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.503 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.503 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.503 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.502 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.501 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.501 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.499 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.499 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.499 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.498 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.497 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.497 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.496 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.495 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.495 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.495 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.494 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.492 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.492 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.491 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.491 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.491 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.490 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.489 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.489 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.488 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.488 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.488 | |
| 1sny | NAP | LD36273p | / | 0.487 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.487 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.486 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.486 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.485 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.480 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.480 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.478 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.478 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.476 | |
| 3sju | NDP | Keto reductase | / | 0.476 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.475 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.474 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.472 | |
| 4qec | NAP | ElxO | / | 0.472 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.471 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.469 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.469 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.469 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.467 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.467 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.466 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.466 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.465 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.464 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.462 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.462 | |
| 3uce | NDP | Dehydrogenase | / | 0.461 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.460 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.459 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.457 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.457 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.457 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.455 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.455 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.455 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.455 | |
| 5dp2 | NAP | CurF | / | 0.455 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.454 | |
| 4qed | NAP | ElxO | / | 0.454 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.453 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.453 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.453 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.452 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.452 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.452 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.452 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.452 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.451 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.451 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.450 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.450 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.446 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.445 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.444 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.444 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.442 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.442 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.442 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.442 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.441 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 |