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 |
|---|---|---|---|
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 1.000 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.663 | |
| 1iy8 | NAD | Levodione reductase | / | 0.616 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.607 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.598 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.598 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.589 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.586 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.586 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.563 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.561 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.558 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.557 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.556 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.554 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.551 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.549 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.547 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.547 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.544 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.543 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.541 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.540 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.538 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.538 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.538 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.536 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.535 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.534 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.534 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.533 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.533 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.533 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.533 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.532 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.532 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.531 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.531 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.531 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.531 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.530 | |
| 3sju | NDP | Keto reductase | / | 0.530 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.529 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.529 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.528 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.528 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.528 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.527 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.525 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.524 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.522 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.522 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.522 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.517 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.516 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.516 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.516 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.515 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.515 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.511 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.510 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.509 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.509 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.509 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.508 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.508 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.505 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.504 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.504 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.504 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.503 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.502 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.502 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.499 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.499 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.498 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.497 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.496 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.495 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.495 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.494 | |
| 1sny | NAP | LD36273p | / | 0.493 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.493 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.492 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.491 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.490 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.490 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.489 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.488 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.488 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.487 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.486 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.486 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.485 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.484 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.484 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.483 | |
| 4qec | NAP | ElxO | / | 0.483 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.482 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.481 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.481 | |
| 4qed | NAP | ElxO | / | 0.481 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.480 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.479 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.478 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.476 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.476 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.476 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.475 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.474 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.474 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.473 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.473 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.473 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.471 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.471 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.471 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.470 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.470 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.468 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.468 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.467 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.466 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.466 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.465 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.465 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.465 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.464 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.464 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.463 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.461 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.461 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.458 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.458 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.458 | |
| 3bmo | NAP | Pteridine reductase | / | 0.458 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.458 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.458 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.456 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.456 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.455 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.455 | |
| 1gd1 | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.453 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.453 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.453 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.453 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.453 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.451 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.450 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.450 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.450 | |
| 3uce | NDP | Dehydrogenase | / | 0.450 | |
| 4o1m | NAD | Enoyl-acyl carrier reductase | / | 0.450 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.449 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.448 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.447 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.446 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.446 | |
| 2ieb | ZID | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.445 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.444 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.444 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 1gyp | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.443 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.443 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.442 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.442 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.442 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.442 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.440 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4kwh | NAP | Reductase homolog | / | 0.440 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |