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 |
|---|---|---|---|
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 1.000 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.641 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.630 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.628 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.622 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.583 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.567 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.557 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.553 | |
| 1iy8 | NAD | Levodione reductase | / | 0.544 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.544 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.542 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.540 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.537 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.534 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.534 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.532 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.528 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.528 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.525 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.523 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.522 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.521 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.521 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.520 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.519 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.516 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.515 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.514 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.513 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.511 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.511 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.511 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.510 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.510 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.509 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.508 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.506 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.505 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.504 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.504 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.504 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.503 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.503 | |
| 1sny | NAP | LD36273p | / | 0.502 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.502 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.499 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.498 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.498 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.498 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.496 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.494 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.494 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.492 | |
| 4qec | NAP | ElxO | / | 0.492 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.491 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.490 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.490 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.490 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.490 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.488 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.488 | |
| 3sju | NDP | Keto reductase | / | 0.487 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.487 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.486 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.485 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.485 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.485 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.485 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.485 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.484 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.484 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.484 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.481 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.481 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.481 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.479 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.479 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.478 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.478 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.478 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.477 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.477 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.476 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.476 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.476 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.476 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.475 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.475 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.475 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.473 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.473 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.471 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.471 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.471 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.471 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.470 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.470 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.469 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.469 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.468 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.468 | |
| 1ybm | NAP | Uncharacterized protein At5g02240 | / | 0.468 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.467 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.467 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.466 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.465 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.465 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.465 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.465 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.465 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.464 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.464 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.463 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.463 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.463 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.463 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.462 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.462 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.461 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.461 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.461 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.461 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.461 | |
| 4qed | NAP | ElxO | / | 0.461 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.460 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.459 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.459 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.459 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.459 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.458 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.457 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.457 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.456 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.456 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.456 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.455 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.455 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.455 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.454 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.454 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.454 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.453 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.453 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.451 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.450 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.450 | |
| 1n7h | NDP | GDP-mannose 4,6 dehydratase 2 | 4.2.1.47 | 0.449 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.448 | |
| 3uce | NDP | Dehydrogenase | / | 0.448 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.448 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.447 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.447 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.447 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.446 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.445 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.442 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.442 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.442 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.442 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.441 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.440 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.440 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.440 |