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 |
|---|---|---|---|
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1e3s | 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 | 0.595 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.584 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.571 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.556 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.553 | |
| 1iy8 | NAD | Levodione reductase | / | 0.552 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.551 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.549 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.545 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.544 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.535 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.532 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.528 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.524 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.524 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.523 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.521 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.521 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.520 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.519 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.515 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.514 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.513 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.512 | |
| 3sx2 | NAD | Uncharacterized protein | / | 0.511 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.510 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.510 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.506 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.503 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.503 | |
| 4qec | NAP | ElxO | / | 0.503 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.502 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.502 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.502 | |
| 3s55 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.500 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.499 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.499 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.498 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.497 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.497 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.495 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.494 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.494 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.493 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.491 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.490 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.490 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.490 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.489 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.489 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.488 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.488 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.487 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.486 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.486 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.485 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.485 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.485 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.484 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.483 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.482 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.481 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.481 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.480 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.480 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.478 | |
| 4cql | NAD | Estradiol 17-beta-dehydrogenase 8 | 1.1.1.62 | 0.478 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.477 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.477 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.477 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.477 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.476 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.476 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.476 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.476 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.476 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.476 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.475 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.474 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.474 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.474 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.473 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.473 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.473 | |
| 1x7h | NDP | Putative ketoacyl reductase | 1.3.1 | 0.472 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.472 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.472 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.472 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.471 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.471 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.470 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.470 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.470 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.470 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.468 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.468 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.468 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.467 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.467 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.466 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.466 | |
| 3sju | NDP | Keto reductase | / | 0.466 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.466 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.466 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.465 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.465 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.464 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.464 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.464 | |
| 3uce | NDP | Dehydrogenase | / | 0.464 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.464 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.464 | |
| 1edo | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase 1, chloroplastic | 1.1.1.100 | 0.463 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.463 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.462 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.462 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.462 | |
| 4ej0 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.462 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.461 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.461 | |
| 1cdo | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.460 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.460 | |
| 3r3s | NAD | Putative oxidoreductase | / | 0.460 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.459 | |
| 1qyv | NAP | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.458 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.458 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.458 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.457 | |
| 3pgx | NAD | Uncharacterized NAD-dependent oxidoreductase MAP_4146 | / | 0.457 | |
| 4bms | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.457 | |
| 4bmv | NAP | Short-chain dehydrogenase | / | 0.457 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.457 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.456 | |
| 1xkq | NDP | Uncharacterized protein | / | 0.455 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.455 | |
| 4ng5 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 5ig2 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.455 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.454 | |
| 1kvr | NAD | UDP-glucose 4-epimerase | 5.1.3.2 | 0.454 | |
| 4gll | NAD | UDP-glucuronic acid decarboxylase 1 | 4.1.1.35 | 0.454 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.453 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.452 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.452 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.451 | |
| 3l77 | NJP | Short-chain alcohol dehydrogenase | / | 0.450 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 4zju | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.450 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.449 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.449 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.449 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.448 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.447 | |
| 2fze | APR | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.446 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.446 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.446 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.446 | |
| 4qed | NAP | ElxO | / | 0.446 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.446 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.446 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.445 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 2ome | NAD | C-terminal-binding protein 2 | / | 0.444 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.444 | |
| 1sny | NAP | LD36273p | / | 0.443 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.443 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.443 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.443 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.442 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.442 | |
| 2hrb | NAP | Carbonyl reductase [NADPH] 3 | 1.1.1.184 | 0.442 | |
| 2q1t | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.442 | |
| 3g49 | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.442 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.442 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 4cpd | NAD | Alcohol dehydrogenase | / | 0.441 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.441 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.440 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.440 |