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 |
|---|---|---|---|
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 1.000 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.610 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.607 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.591 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.591 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.589 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.575 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.568 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.557 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.555 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.550 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.550 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.549 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.548 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.548 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.547 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.546 | |
| 1iy8 | NAD | Levodione reductase | / | 0.543 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.540 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.540 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.539 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.539 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.531 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.530 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.530 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.529 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.526 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.526 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.525 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.524 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.522 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.520 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.519 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.518 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.518 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.517 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.517 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.517 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.516 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.516 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.515 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.514 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.513 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.513 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.512 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.512 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.511 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.509 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.508 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.508 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.506 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.505 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.503 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.502 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.501 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.501 | |
| 4qec | NAP | ElxO | / | 0.501 | |
| 1sny | NAP | LD36273p | / | 0.500 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.500 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.499 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.495 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.494 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.492 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.492 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.491 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.490 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.490 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.489 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.489 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.489 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.488 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.488 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.487 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.486 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.486 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.483 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.483 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.483 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.482 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.482 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.481 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.481 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.481 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.481 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.480 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.479 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.479 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.478 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.478 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.478 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.477 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.476 | |
| 4qed | NAP | ElxO | / | 0.476 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.476 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.472 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.471 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.471 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.470 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.470 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.470 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.469 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.468 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.468 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.468 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.468 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.467 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.467 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.467 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.467 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.466 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.465 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.464 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.464 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.463 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.463 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.463 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.462 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.462 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.462 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.461 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.461 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.461 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.460 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.460 | |
| 3sju | NDP | Keto reductase | / | 0.460 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.459 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.458 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.458 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.458 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.457 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.456 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.456 | |
| 3uce | NDP | Dehydrogenase | / | 0.456 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.456 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.455 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.455 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.454 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.453 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.452 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.451 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.451 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.451 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.450 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.450 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.449 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.449 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.448 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.448 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.448 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.447 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.447 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.446 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.446 | |
| 3dmt | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.446 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.446 | |
| 1mj9 | COA | Histone acetyltransferase ESA1 | / | 0.445 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.445 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.445 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.444 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.443 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.443 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.443 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.443 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.443 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.442 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.442 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.441 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.441 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.440 |