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 |
|---|---|---|---|
| 4yag | NAI | C alpha-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4yag | NAI | C alpha-dehydrogenase | / | 1.000 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.902 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.574 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.540 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.538 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.532 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.532 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.531 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.531 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.530 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.529 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.528 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.528 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.527 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.526 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.525 | |
| 1iy8 | NAD | Levodione reductase | / | 0.524 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.523 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.522 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.521 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.520 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.520 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.519 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.519 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.518 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.518 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.518 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.517 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.517 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.516 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.515 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.515 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.515 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.514 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.514 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.513 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.513 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.509 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.508 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.508 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.505 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.505 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.505 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.504 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.504 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.503 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.502 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.501 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.500 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.500 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.499 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.499 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.498 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.497 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.497 | |
| 1sny | NAP | LD36273p | / | 0.496 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.496 | |
| 4qec | NAP | ElxO | / | 0.496 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.495 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.495 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.494 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.494 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.494 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.493 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.492 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.492 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.490 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.490 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.490 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.490 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.489 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.489 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.488 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.487 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.487 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.487 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.487 | |
| 3sju | NDP | Keto reductase | / | 0.486 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.486 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.486 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.486 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.485 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.485 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.484 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.483 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.482 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.482 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.482 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.482 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.482 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.481 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.481 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.480 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.480 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.480 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.479 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.479 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.479 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.479 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.478 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.478 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.477 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.477 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.476 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.476 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.476 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.476 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.475 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.475 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.475 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.475 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.474 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.474 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.472 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.472 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.471 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.469 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.469 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.469 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.469 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.468 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.468 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.468 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.467 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.467 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.466 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.465 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.465 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.465 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.464 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.464 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.464 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.463 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.459 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.459 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.459 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.457 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.456 | |
| 3uce | NDP | Dehydrogenase | / | 0.456 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.455 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.455 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.455 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.455 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.455 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.454 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.454 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.453 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.452 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.452 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.452 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.451 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.451 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.451 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.450 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.449 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.448 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.447 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.446 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.445 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.444 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.444 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.442 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.442 | |
| 1nqo | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.441 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4qed | NAP | ElxO | / | 0.441 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.440 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 |