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 |
|---|---|---|---|
| 5lc1 | NAD | L-threonine 3-dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 1.000 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.593 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.569 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.566 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.552 | |
| 2wsb | NAD | Galactitol dehydrogenase | / | 0.528 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.527 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.522 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.514 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.510 | |
| 1iy8 | NAD | Levodione reductase | / | 0.508 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.507 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.505 | |
| 2ewm | NAD | (S)-1-Phenylethanol dehydrogenase | 1.1.1.311 | 0.504 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.502 | |
| 1u7t | TDT | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.501 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.500 | |
| 1wnt | NAP | L-xylulose reductase | 1.1.1.10 | 0.495 | |
| 1pr9 | NAP | L-xylulose reductase | 1.1.1.10 | 0.492 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.491 | |
| 1nff | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.489 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.489 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.489 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.488 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.487 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.487 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 2ag5 | NAD | 3-hydroxybutyrate dehydrogenase type 2 | / | 0.485 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.485 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.484 | |
| 3d3w | NAP | L-xylulose reductase | 1.1.1.10 | 0.482 | |
| 2ekp | NAD | 2-deoxy-D-gluconate 3-dehydrogenase | / | 0.480 | |
| 3nug | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.479 | |
| 3a9w | NAD | NDP-sugar epimerase | / | 0.478 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.478 | |
| 2yut | NAP | Putative short-chain oxidoreductase | / | 0.477 | |
| 3qwf | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.477 | |
| 4yai | NAI | C alpha-dehydrogenase | / | 0.477 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.474 | |
| 4fn4 | NAD | Short chain dehydrogenase | / | 0.474 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.473 | |
| 3iah | NAP | Putative oxoacyl-(Acyl carrier protein) reductase | / | 0.473 | |
| 3qrw | NDP | Putative ketoacyl reductase | 1.3.1 | 0.473 | |
| 1cyd | NDP | Carbonyl reductase [NADPH] 2 | 1.1.1.184 | 0.472 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.472 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.470 | |
| 4fj2 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.470 | |
| 4is3 | NAD | 3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 | 1.17.98.1 | 0.470 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.468 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.467 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.465 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.465 | |
| 4yag | NAI | C alpha-dehydrogenase | / | 0.464 | |
| 2ydx | NAP | Methionine adenosyltransferase 2 subunit beta | / | 0.463 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.462 | |
| 1b14 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.461 | |
| 1n5d | NDP | Carbonyl reductase [NADPH] 1 | / | 0.461 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.461 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.461 | |
| 4fj0 | NAP | 17beta-hydroxysteroid dehydrogenase | / | 0.460 | |
| 3vdq | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.458 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.458 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.458 | |
| 1g0n | NDP | Tetrahydroxynaphthalene reductase | 1.1.1.252 | 0.455 | |
| 2q2q | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.455 | |
| 4dc1 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.455 | |
| 4qec | NAP | ElxO | / | 0.455 | |
| 3w8d | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.454 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.454 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.452 | |
| 4dmm | NAP | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.452 | |
| 3rku | NAP | NADP-dependent 3-hydroxy acid dehydrogenase | / | 0.451 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.450 | |
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.450 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.450 | |
| 4j7u | NAP | Sepiapterin reductase | 1.1.1.153 | 0.450 | |
| 1gyp | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.449 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 2bd0 | NAP | Sepiapterin reductase | / | 0.448 | |
| 4j7x | NAP | Sepiapterin reductase | 1.1.1.153 | 0.448 | |
| 3sju | NDP | Keto reductase | / | 0.447 | |
| 4b8z | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.446 | |
| 1ae1 | NAP | Tropinone reductase 1 | / | 0.445 | |
| 1hzz | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.445 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.445 | |
| 1oaa | NAP | Sepiapterin reductase | 1.1.1.153 | 0.444 | |
| 2ztl | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.444 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.443 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.443 | |
| 3p19 | NDP | Putative blue fluorescent protein | / | 0.443 | |
| 1sny | NAP | LD36273p | / | 0.442 | |
| 5jyd | NAD | Short chain dehydrogenase | / | 0.442 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.441 | |
| 4al4 | W7E | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.441 | |
| 4hwk | NAP | Sepiapterin reductase | 1.1.1.153 | 0.441 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.440 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.440 | |
| 2q2v | NAD | Beta-D-hydroxybutyrate dehydrogenase | / | 0.440 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.440 | |
| 3w8f | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.440 |