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 |
|---|---|---|---|
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 1.000 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.633 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.603 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.598 | |
| 1iy8 | NAD | Levodione reductase | / | 0.593 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.589 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.589 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.582 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.581 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.575 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.566 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.562 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.561 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.559 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.558 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.557 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.556 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.552 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.551 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.542 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.541 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.540 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.539 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.538 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.537 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.536 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.536 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.534 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.534 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.533 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.533 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.533 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.531 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.531 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.531 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.530 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.529 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.529 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.528 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.528 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.528 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.528 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.527 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.527 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.526 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.526 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.526 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.525 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.524 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.524 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.524 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.523 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.521 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.520 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.517 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.517 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.516 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.516 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.515 | |
| 3sju | NDP | Keto reductase | / | 0.515 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.514 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.513 | |
| 4qec | NAP | ElxO | / | 0.513 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.512 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.512 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.511 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.511 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.511 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.510 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.510 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.510 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.508 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.508 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.508 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.506 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.506 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.505 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.505 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.505 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.504 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.503 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.503 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.502 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.502 | |
| 4qed | NAP | ElxO | / | 0.501 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.500 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.499 | |
| 1sny | NAP | LD36273p | / | 0.497 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.497 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.495 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.495 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.495 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.494 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.494 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.494 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.493 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.492 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.491 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.491 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.491 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.490 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.490 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.489 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.489 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.487 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.487 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.487 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.487 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.487 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.486 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.483 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.483 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.483 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.482 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.482 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.482 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.481 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.481 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.481 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.480 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.480 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.479 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.479 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.479 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.478 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.477 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.476 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.476 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.476 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.476 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.475 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.474 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.474 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.473 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.473 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.472 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.471 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.470 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.470 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.470 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.469 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.469 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.468 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.468 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.467 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.466 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.465 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.465 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.463 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.462 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.461 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.461 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.460 | |
| 2x6t | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.460 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.460 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.459 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.457 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.457 | |
| 3uce | NDP | Dehydrogenase | / | 0.457 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.457 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 1yba | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.455 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.455 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.454 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.453 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.453 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.453 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.452 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.452 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.452 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.450 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.449 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.447 | |
| 3bmo | NAP | Pteridine reductase | / | 0.447 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.447 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.446 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.446 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.446 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.446 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.445 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.445 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.444 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.444 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.444 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.444 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.443 | |
| 4bkq | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.443 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.442 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.441 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.441 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.441 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.441 | |
| 3lvf | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.440 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.440 |