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 |
|---|---|---|---|
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.664 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.653 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.642 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.641 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.630 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.591 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.583 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.576 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.576 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.573 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.570 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.570 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.570 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.569 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.566 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.566 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.565 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.560 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.558 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.557 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.557 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.553 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.553 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.552 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.551 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.551 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.551 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.550 | |
| 1iy8 | NAD | Levodione reductase | / | 0.549 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.549 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.548 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.548 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.547 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.546 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.545 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.540 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.540 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.539 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.538 | |
| 3sju | NDP | Keto reductase | / | 0.538 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.537 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.537 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.537 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.537 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.536 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.535 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.535 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.535 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.534 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.534 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.534 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.534 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.534 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.532 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.532 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.531 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.531 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.531 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.530 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.529 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.529 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.528 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.528 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.528 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.528 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.527 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.527 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.526 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.525 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.524 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.523 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.523 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.523 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.523 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.522 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.521 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.521 | |
| 4qec | NAP | ElxO | / | 0.521 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.520 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.520 | |
| 1sny | NAP | LD36273p | / | 0.519 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.519 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.518 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.518 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.517 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.516 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.516 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.513 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.513 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.513 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.512 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.511 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.510 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.510 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.509 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.508 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.507 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.507 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.506 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.504 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.503 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.503 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.503 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.502 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.501 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.500 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.499 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.499 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.497 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.497 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.495 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.494 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.493 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.491 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.491 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.490 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.489 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.485 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.485 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.485 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.484 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.484 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.484 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.484 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.483 | |
| 5dp2 | NAP | CurF | / | 0.483 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.482 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.481 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.481 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.481 | |
| 3uce | NDP | Dehydrogenase | / | 0.478 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.476 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 1kev | NDP | NADP-dependent isopropanol dehydrogenase | 1.1.1.80 | 0.475 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.475 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.475 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.474 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.474 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.473 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.472 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.472 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.472 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.472 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.471 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.470 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.470 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.469 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.469 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.467 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.465 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.465 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.465 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.465 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.465 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.464 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.464 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.464 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.463 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.463 | |
| 3bmo | NAP | Pteridine reductase | / | 0.462 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.461 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.460 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.460 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.460 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.459 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.459 | |
| 4qed | NAP | ElxO | / | 0.458 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.457 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.456 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.456 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.456 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.456 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.456 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.455 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.455 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.454 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.453 | |
| 2c0c | NAP | Prostaglandin reductase 3 | 1 | 0.452 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.452 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.451 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.449 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.449 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.449 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.448 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.448 | |
| 1t2a | NDP | GDP-mannose 4,6 dehydratase | 4.2.1.47 | 0.448 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.448 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.448 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.446 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.444 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.444 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.444 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.443 | |
| 2jkv | NAP | 6-phosphogluconate dehydrogenase, decarboxylating | 1.1.1.44 | 0.442 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.442 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.441 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.441 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.441 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.441 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.440 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.440 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.440 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.440 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.440 |