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 |
|---|---|---|---|
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.680 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.632 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.628 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.624 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.621 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.607 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.593 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.575 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.573 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.567 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.567 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.565 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.560 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.558 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.558 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.557 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.556 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.555 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.554 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.554 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.552 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.552 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.552 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.552 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.551 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.550 | |
| 1iy8 | NAD | Levodione reductase | / | 0.549 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.548 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.547 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.547 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.546 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.544 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.544 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.543 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.543 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.542 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.541 | |
| 3sju | NDP | Keto reductase | / | 0.538 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.537 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.536 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.536 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.535 | |
| 1sny | NAP | LD36273p | / | 0.535 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.535 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.534 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.534 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.533 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.533 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.532 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.532 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.531 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.531 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.530 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.528 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.525 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.525 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.524 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.524 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.523 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.522 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.520 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.520 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.519 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.518 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.516 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.516 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.516 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.514 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.514 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.513 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.512 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.512 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.512 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.511 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.511 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.511 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.510 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.510 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.508 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.507 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.506 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.506 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.506 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.506 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.503 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.502 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.502 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.501 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.500 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.499 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.498 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.498 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.498 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.497 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.496 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.496 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.495 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.495 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.494 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.494 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.493 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.493 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.492 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.491 | |
| 4qec | NAP | ElxO | / | 0.491 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.490 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.490 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.490 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.490 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.488 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.488 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.487 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.485 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.485 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.484 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.484 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.484 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.483 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.483 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.482 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.480 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.479 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.479 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.479 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.477 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.476 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.476 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.476 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.475 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.474 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.474 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.472 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.472 | |
| 3uce | NDP | Dehydrogenase | / | 0.472 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.471 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.471 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.470 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.468 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.467 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.465 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.465 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.462 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.461 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.461 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.460 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.460 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.460 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.460 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.459 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.459 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.458 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.458 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.457 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.457 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.457 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.456 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.456 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.456 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.456 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.455 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.455 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.454 | |
| 3bmo | NAP | Pteridine reductase | / | 0.453 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.451 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.451 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.450 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.450 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.450 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.450 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.449 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.448 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.448 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.448 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.448 | |
| 4qed | NAP | ElxO | / | 0.448 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.447 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.447 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.447 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.446 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.446 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.446 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.445 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.445 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.444 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.444 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.444 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.444 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.444 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.443 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.441 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.441 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.440 |