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 |
|---|---|---|---|
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 1.000 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.698 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.566 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.556 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.552 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.549 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.548 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.546 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.546 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.543 | |
| 1iy8 | NAD | Levodione reductase | / | 0.543 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.543 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.542 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.542 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.542 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.539 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.538 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.536 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.536 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.534 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.529 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.527 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.527 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.526 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.525 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.525 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.525 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.524 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.523 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.522 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.522 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.520 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.518 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.518 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.517 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.516 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.516 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.514 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.513 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.512 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.510 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.509 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.509 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.508 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.508 | |
| 1sny | NAP | LD36273p | / | 0.506 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.506 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.506 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.506 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.505 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.505 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.503 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.503 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.503 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.503 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.503 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.502 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.502 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.501 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.500 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.500 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.499 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.499 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.499 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.498 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.497 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.496 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.496 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.496 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.496 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.495 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.495 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.494 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.494 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.494 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.494 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.493 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.492 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.491 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.491 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.491 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.490 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.490 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.489 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.487 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.486 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.486 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.485 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.484 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.483 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.483 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.483 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.483 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.483 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.482 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.482 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.482 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.482 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.482 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.481 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.481 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.480 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.480 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.479 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.478 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.478 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.478 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.478 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.478 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.477 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.477 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.477 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.476 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.475 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.475 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.475 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.473 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.473 | |
| 4qec | NAP | ElxO | / | 0.473 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.472 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.472 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.471 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.471 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.471 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.471 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.471 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.471 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.470 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.469 | |
| 3uce | NDP | Dehydrogenase | / | 0.468 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.467 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.466 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.464 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.464 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.464 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.464 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.464 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.463 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.463 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.461 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.461 | |
| 1fy7 | COA | Histone acetyltransferase ESA1 | / | 0.460 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.460 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.460 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.459 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.459 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.458 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.458 | |
| 3sju | NDP | Keto reductase | / | 0.457 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.457 | |
| 3u4c | NDP | NADPH-dependent reductase BacG | / | 0.457 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.456 | |
| 3hja | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.456 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.456 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.455 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.455 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.455 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.454 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.453 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.450 | |
| 4e5y | NDP | GDP-L-fucose synthase | 1.1.1.271 | 0.450 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.450 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.449 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.449 | |
| 1k6p | XN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.447 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.447 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 1mjb | ACO | Histone acetyltransferase ESA1 | / | 0.446 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.445 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.445 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.445 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.443 | |
| 2ozu | ACO | Histone acetyltransferase KAT6A | / | 0.443 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.443 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 4qed | NAP | ElxO | / | 0.443 | |
| 1mja | COA | Histone acetyltransferase ESA1 | / | 0.442 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.442 | |
| 3l4s | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.442 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.442 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.442 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.441 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.440 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.440 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.440 |