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 |
|---|---|---|---|
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 1.000 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.666 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.662 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.640 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.632 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.591 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.588 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.570 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.553 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.546 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.545 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.544 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.543 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.539 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.538 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.537 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.535 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.535 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.529 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.528 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.524 | |
| 1x7g | NAP | Putative ketoacyl reductase | 1.3.1 | 0.520 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.519 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.518 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.518 | |
| 1iy8 | NAD | Levodione reductase | / | 0.517 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.516 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.515 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.514 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.512 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.512 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.511 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.510 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.509 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.508 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.508 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.507 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.506 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.506 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.505 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.505 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.504 | |
| 2jah | NDP | Clavaldehyde dehydrogenase | / | 0.503 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.503 | |
| 3sju | NDP | Keto reductase | / | 0.501 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.499 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.499 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.499 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.499 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.498 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.498 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.497 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.497 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.497 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.496 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.496 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.496 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.496 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.496 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.496 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.496 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.495 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.494 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.494 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.493 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.493 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.493 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.493 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.492 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.492 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.492 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.490 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.489 | |
| 4qec | NAP | ElxO | / | 0.489 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.488 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.488 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.487 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.485 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.485 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.483 | |
| 3uce | NDP | Dehydrogenase | / | 0.483 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.482 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.482 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.482 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.482 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.481 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.480 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.480 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.480 | |
| 4o0l | NDP | NADPH-dependent 3-quinuclidinone reductase | / | 0.479 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.478 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.478 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.478 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.477 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.476 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.476 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.475 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.474 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.474 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.473 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.471 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.469 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.469 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.469 | |
| 4qed | NAP | ElxO | / | 0.469 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.468 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.468 | |
| 1sny | NAP | LD36273p | / | 0.468 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.468 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.467 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.467 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.466 | |
| 4lis | NAD | UDP-glucose 4-epimerase (Eurofung) | / | 0.466 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.465 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.465 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.465 | |
| 4oxy | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.464 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.463 | |
| 4imp | NDP | Polyketide synthase extender modules 3-4 | / | 0.463 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.462 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.462 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.460 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.460 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.459 | |
| 4pvd | NDP | NADPH-dependent methylglyoxal reductase GRE2 | / | 0.459 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.456 | |
| 5dbg | NAD | Iridoid synthase | 1.3.1.99 | 0.456 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.456 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.455 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.454 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.453 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.453 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.453 | |
| 5dcy | NAP | Iridoid synthase | 1.3.1.99 | 0.453 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.452 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.452 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.450 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.450 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.450 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.449 | |
| 3tn7 | NJP | Short-chain alcohol dehydrogenase | / | 0.448 | |
| 1fdu | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.447 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.447 | |
| 5emh | NAP | Iridoid synthase | 1.3.1.99 | 0.447 | |
| 5koi | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.447 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.446 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.445 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.445 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.445 | |
| 4m87 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.445 | |
| 3bmo | NAP | Pteridine reductase | / | 0.444 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.444 | |
| 2aqk | NAI | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.443 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.443 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.442 | |
| 2x86 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.441 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.441 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.441 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.440 |