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 |
|---|---|---|---|
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 1.000 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.574 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.572 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.566 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.559 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.558 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.553 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.551 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.550 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.547 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.547 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.547 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.543 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.542 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.541 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.540 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.540 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.539 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.537 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.533 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.532 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.531 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.530 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.530 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.529 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.528 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.528 | |
| 1iy8 | NAD | Levodione reductase | / | 0.527 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.527 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.527 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.527 | |
| 3sju | NDP | Keto reductase | / | 0.526 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.526 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.523 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.523 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.521 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.520 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.519 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.518 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.517 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.515 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.515 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.515 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.510 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.508 | |
| 1sny | NAP | LD36273p | / | 0.506 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.506 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.504 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.504 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.504 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.503 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.502 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.502 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.501 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.500 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.500 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.500 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.499 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.499 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.498 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.498 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.497 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.496 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.496 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.495 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.495 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.495 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.494 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.492 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.492 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.491 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.490 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.489 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.489 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.489 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.488 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.487 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.487 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.485 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.485 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.484 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.484 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.484 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.483 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.483 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.482 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.482 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.482 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.481 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.480 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.480 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.479 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.479 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.479 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.479 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.478 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.478 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.476 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.475 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.475 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.474 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.474 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.474 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.473 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.472 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.472 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.471 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.471 | |
| 4qec | NAP | ElxO | / | 0.471 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.470 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.470 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.470 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.469 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.467 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.466 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.465 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.465 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.464 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.464 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.463 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.463 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.462 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.462 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.461 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.461 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.461 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.460 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.460 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.459 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.459 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.456 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.456 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.455 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.454 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.453 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.453 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.452 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.451 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.450 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.449 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.448 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.448 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.447 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.447 | |
| 2gn8 | NAP | UDP-N-acetylglucosamine 4,6-dehydratase (inverting) | 4.2.1.115 | 0.446 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.446 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.446 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.445 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.445 | |
| 1u3v | NAD | Alcohol dehydrogenase 1B | 1.1.1.1 | 0.444 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.444 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.443 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.443 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.442 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.441 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.440 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.440 |