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 |
|---|---|---|---|
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity 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 | / | 0.623 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.615 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.607 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.592 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.575 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.565 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.556 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.552 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.551 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.550 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.550 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.549 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.549 | |
| 1iy8 | NAD | Levodione reductase | / | 0.548 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.547 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.546 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.546 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.546 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.542 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.541 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.540 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.538 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.538 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.538 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.537 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.535 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.533 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.532 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.531 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.531 | |
| 1sny | NAP | LD36273p | / | 0.530 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.530 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.530 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.527 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.527 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.527 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.526 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.526 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.524 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.524 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.523 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.523 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.523 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.522 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.522 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.520 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.517 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.516 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.515 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.514 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.513 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.512 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.510 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.509 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.507 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.507 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.507 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.506 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.505 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.505 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.504 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.503 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.503 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.503 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.503 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.500 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.499 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.498 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.497 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.497 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.497 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.497 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.495 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.495 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.494 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.494 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.493 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.491 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.490 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.490 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.490 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.489 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.489 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.487 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.487 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.487 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.486 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.486 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.486 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.486 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.486 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.485 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.485 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.484 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.483 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.482 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.482 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.482 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.481 | |
| 4qec | NAP | ElxO | / | 0.481 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.480 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.477 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.477 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.476 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.475 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.475 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.474 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.473 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.473 | |
| 2ie0 | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.470 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.470 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.469 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.468 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.467 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.466 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.465 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.464 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.464 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.464 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.463 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.461 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.461 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.460 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.460 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.460 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.460 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.458 | |
| 1fm4 | DXC | Major pollen allergen Bet v 1-L | / | 0.457 | |
| 2h9i | EAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.457 | |
| 3uce | NDP | Dehydrogenase | / | 0.457 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.456 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.456 | |
| 1v35 | NAI | Enoyl-ACP reductase | / | 0.455 | |
| 2aqi | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.455 | |
| 3e5r | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1, cytosolic | 1.2.1.12 | 0.454 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.453 | |
| 1xkv | ATP | Phosphoenolpyruvate carboxykinase (ATP) | / | 0.453 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1vrw | NAI | Enoyl-ACP reductase | / | 0.452 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 1k7l | 544 | Peroxisome proliferator-activated receptor alpha | / | 0.451 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 4qed | NAP | ElxO | / | 0.451 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.450 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.450 | |
| 3cos | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.448 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.447 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.447 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.447 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.446 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.446 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.444 | |
| 3bmo | NAP | Pteridine reductase | / | 0.444 | |
| 4a83 | DXC | Major pollen allergen Bet v 1-A | / | 0.444 | |
| 1uay | ADN | Oxidoreductase | / | 0.443 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.443 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.443 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.442 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 3uyl | TYD | Probable NDP-rhamnosyltransferase | / | 0.442 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.442 | |
| 5adh | APR | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 1osv | CHC | Bile acid receptor | / | 0.441 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3cif | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.441 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.440 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.440 |