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 |
|---|---|---|---|
| 4yai | NAI | C alpha-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4yai | NAI | C alpha-dehydrogenase | / | 1.000 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.898 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.566 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.539 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.533 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.529 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.529 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.525 | |
| 1iy8 | NAD | Levodione reductase | / | 0.524 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.524 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.524 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.523 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.523 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.523 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.522 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.522 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.518 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.518 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.517 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.516 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.515 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.514 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.513 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.513 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.512 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.511 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.511 | |
| 4qec | NAP | ElxO | / | 0.511 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.511 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.510 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.509 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.509 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.508 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.507 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.507 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.506 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.506 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.505 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.505 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.504 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.503 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.503 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.502 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.501 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.501 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.501 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.500 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.497 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.497 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.497 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.497 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.496 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.496 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.495 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.494 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.493 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.493 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.493 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.492 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.492 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.491 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.489 | |
| 3sju | NDP | Keto reductase | / | 0.489 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.489 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.488 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.488 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.488 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.487 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.487 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.486 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.486 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.486 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.485 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.485 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.484 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.484 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.484 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.484 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.482 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.481 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.480 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.480 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.480 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.479 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.479 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.479 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.478 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.477 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.477 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.477 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.477 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.477 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.477 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.476 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.475 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.475 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.475 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.475 | |
| 1sny | NAP | LD36273p | / | 0.474 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.474 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.473 | |
| 1nai | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.473 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.472 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.472 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.472 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.471 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.471 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.469 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.468 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.468 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.468 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.467 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.467 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.466 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.466 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.465 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.465 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.465 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.465 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.464 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.463 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.463 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.460 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.459 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.459 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.459 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.458 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.457 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.457 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.455 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.454 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.453 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.453 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.452 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.452 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.451 | |
| 4fc7 | NAP | Peroxisomal 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.451 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.450 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.450 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.450 | |
| 1nah | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.449 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.448 | |
| 2o23 | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.447 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.446 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.445 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.444 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.443 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.443 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.443 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.442 | |
| 3uce | NDP | Dehydrogenase | / | 0.442 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.441 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.441 |