sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| 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 | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1e3s | 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 | 0.583 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.578 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.539 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.537 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.530 | |
| 1iy8 | NAD | Levodione reductase | / | 0.528 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.528 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.526 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.522 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.514 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.514 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.504 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.503 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.500 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.499 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.498 | |
| 2dkn | NAI | 3-alpha-hydroxysteroid dehydrogenase | / | 0.496 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.496 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.493 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.492 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.491 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.488 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.486 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.484 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.484 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.484 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.482 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.479 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.479 | |
| 4b79 | NAD | Probable short-chain dehydrogenase | / | 0.478 | |
| 4qec | NAP | ElxO | / | 0.478 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.477 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.477 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.476 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.475 | |
| 3geg | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.474 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.474 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.473 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.473 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.471 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.471 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.471 | |
| 1gee | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.470 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.469 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.469 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.469 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.469 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.469 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.467 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.466 | |
| 3o4r | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.465 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.464 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.464 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.464 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.463 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.463 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.463 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.461 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.461 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.460 | |
| 3ai2 | NDP | NADPH-sorbose reductase | / | 0.460 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.460 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.459 | |
| 1gco | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.458 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.458 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.457 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.457 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.457 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.457 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.457 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.457 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.456 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.456 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.456 | |
| 1nfr | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.455 | |
| 4qed | NAP | ElxO | / | 0.455 | |
| 3sxp | NAD | ADP-L-glycero-D-mannoheptose-6-epimerase | / | 0.454 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.453 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.453 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.453 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.453 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.452 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.451 | |
| 1xg5 | NAP | Dehydrogenase/reductase SDR family member 11 | / | 0.450 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.450 | |
| 3ijr | NAD | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.450 | |
| 1rwb | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.449 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.448 | |
| 1vl8 | NAP | Oxidoreductase, short chain dehydrogenase/reductase family | / | 0.447 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.447 | |
| 3sju | NDP | Keto reductase | / | 0.446 | |
| 4idg | NAD | Putative UDP-glucose 4-epimerase | / | 0.446 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.445 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.445 | |
| 4i5e | NAP | Alclohol dehydrogenase/short-chain dehydrogenase | / | 0.445 | |
| 1i2b | NAD | UDP-sulfoquinovose synthase, chloroplastic | 3.13.1.1 | 0.444 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.444 | |
| 3uce | NDP | Dehydrogenase | / | 0.443 | |
| 3uxy | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 5idw | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.443 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.442 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.442 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.442 | |
| 3tsc | NAD | Uncharacterized protein | / | 0.442 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.441 | |
| 1xse | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.441 | |
| 4fj1 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.441 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.440 |