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 |
|---|---|---|---|
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1sow | NAD | L-lactate dehydrogenase | 1.1.1.27 | 1.000 | |
| 1pzg | A3D | Lactate dehydrogenase | / | 0.627 | |
| 1pzf | A3D | Lactate dehydrogenase | / | 0.626 | |
| 1t2d | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.623 | |
| 4nd2 | A3D | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.612 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.582 | |
| 2hjr | APR | Malate dehydrogenase, adjacent gene encodes predicted lactate dehydrogenase | / | 0.582 | |
| 4wlu | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.574 | |
| 4nd4 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.573 | |
| 2fn7 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.564 | |
| 5mdh | NAD | Malate dehydrogenase, cytoplasmic | 1.1.1.37 | 0.558 | |
| 2aa3 | AP0 | L-lactate dehydrogenase | / | 0.551 | |
| 4wlo | NAI | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.546 | |
| 4wlv | NAD | Malate dehydrogenase, mitochondrial | 1.1.1.37 | 0.546 | |
| 1ie3 | NAD | Malate dehydrogenase | / | 0.545 | |
| 5a1t | NAI | L-lactate dehydrogenase | / | 0.534 | |
| 4ajp | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.526 | |
| 4ajo | 88N | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.522 | |
| 1zem | NAD | Xylitol dehydrogenase | / | 0.509 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.498 | |
| 4dl9 | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.497 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.495 | |
| 1hyh | NAD | L-2-hydroxyisocaproate dehydrogenase | / | 0.494 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.493 | |
| 2fze | APR | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.492 | |
| 4dlb | NAD | S-(hydroxymethyl)glutathione dehydrogenase | / | 0.492 | |
| 4okn | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.491 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.490 | |
| 1pzh | NAD | Lactate dehydrogenase | / | 0.488 | |
| 4yr9 | NAD | L-threonine 3-dehydrogenase, mitochondrial | 1.1.1.103 | 0.486 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.485 | |
| 3rj9 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.485 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.484 | |
| 5lc1 | NAD | L-threonine 3-dehydrogenase | / | 0.482 | |
| 3a4v | NAD | NDP-sugar epimerase | / | 0.480 | |
| 1e6w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.479 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.479 | |
| 2ahr | NAP | Pyrroline-5-carboxylate reductase | / | 0.477 | |
| 2jhf | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.477 | |
| 4xgi | NAD | Glutamate dehydrogenase | / | 0.476 | |
| 4c4o | NAD | SADH | / | 0.475 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.474 | |
| 1yqx | NAP | Sinapyl alcohol dehydrogenase | / | 0.474 | |
| 3ggp | NAD | Prephenate dehydrogenase | / | 0.474 | |
| 4gkv | NAD | Alcohol dehydrogenase, propanol-preferring | 1.1.1.1 | 0.474 | |
| 4nfh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.474 | |
| 1e3s | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.473 | |
| 3qvx | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.473 | |
| 1adc | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.472 | |
| 3rj5 | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.472 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.472 | |
| 4w6z | 8ID | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.472 | |
| 1mg5 | NAI | Alcohol dehydrogenase | 1.1.1.1 | 0.471 | |
| 2vhx | NAD | Alanine dehydrogenase | 1.4.1.1 | 0.471 | |
| 3ak4 | NAD | NADH-dependent quinuclidinone reductase | / | 0.470 | |
| 1b16 | NAQ | Alcohol dehydrogenase | 1.1.1.1 | 0.469 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.469 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.468 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.468 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.468 | |
| 1h2b | NAJ | NAD-dependent alcohol dehydrogenase | / | 0.467 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.467 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.466 | |
| 2vhv | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.466 | |
| 4egb | NAD | dTDP-glucose 4,6-dehydratase | / | 0.466 | |
| 2hsd | NAD | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.465 | |
| 3aw9 | NAD | NAD-dependent epimerase/dehydratase | / | 0.465 | |
| 3ggo | NAI | Prephenate dehydrogenase | / | 0.465 | |
| 3jv7 | NAD | Secondary alcohol dehydrogenase | / | 0.465 | |
| 3ruc | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.463 | |
| 1e3w | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.462 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.462 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.462 | |
| 1adb | CND | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.461 | |
| 3ajr | NAD | NDP-sugar epimerase | / | 0.461 | |
| 3abi | NAD | Uncharacterized protein | / | 0.460 | |
| 3cin | NAD | Myo-inositol-1-phosphate synthase-related protein | / | 0.460 | |
| 3wds | NAD | NADH-dependent quinuclidinone reductase | / | 0.460 | |
| 4cr8 | NAD | N-acylmannosamine 1-dehydrogenase | 1.1.1.233 | 0.460 | |
| 4nbu | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.460 | |
| 4xqc | NAD | Homospermidine synthase | 2.5.1.44 | 0.460 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.459 | |
| 3ruh | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.459 | |
| 1bxk | NAD | dTDP-glucose 4,6-dehydratase 2 | / | 0.458 | |
| 2dte | NAI | Glucose 1-dehydrogenase related protein | / | 0.458 | |
| 2xaa | NAD | Secondary alcohol dehydrogenase | / | 0.458 | |
| 5jy1 | NAD | Putative short-chain dehydrogenase/reductase | / | 0.458 | |
| 2c59 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.457 | |
| 3ksd | NAD | Glyceraldehyde-3-phosphate dehydrogenase 1 | / | 0.457 | |
| 3ru7 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.457 | |
| 4iqg | NAP | Short-chain dehydrogenase/reductase SDR | / | 0.457 | |
| 1a71 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.456 | |
| 1iy8 | NAD | Levodione reductase | / | 0.456 | |
| 1r37 | NAD | NAD-dependent alcohol dehydrogenase | 1.1.1.1 | 0.456 | |
| 2a94 | AP0 | L-lactate dehydrogenase | 1.1.1.27 | 0.456 | |
| 2c54 | NAD | GDP-mannose 3,5-epimerase | 5.1.3.18 | 0.456 | |
| 2gdz | NAD | 15-hydroxyprostaglandin dehydrogenase [NAD(+)] | 1.1.1.141 | 0.456 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.456 | |
| 2hun | NAD | 336aa long hypothetical dTDP-glucose 4,6-dehydratase | / | 0.455 | |
| 1eq2 | NAP | ADP-L-glycero-D-manno-heptose-6-epimerase | / | 0.454 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.454 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.454 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.453 | |
| 5env | NAD | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.453 | |
| 1b15 | NAE | Alcohol dehydrogenase | 1.1.1.1 | 0.451 | |
| 1agn | NAD | Alcohol dehydrogenase class 4 mu/sigma chain | 1.1.1.1 | 0.450 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.450 | |
| 1qxs | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.450 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.450 | |
| 3lu1 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.450 | |
| 1sby | NAD | Alcohol dehydrogenase | 1.1.1.1 | 0.449 | |
| 1yqd | NAP | Sinapyl alcohol dehydrogenase | / | 0.449 | |
| 2ztm | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.449 | |
| 3rua | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.449 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.449 | |
| 4rf2 | NAP | NADPH dependent R-specific alcohol dehydrogenase | / | 0.449 | |
| 4xrg | NAD | Homospermidine synthase | 2.5.1.44 | 0.449 | |
| 3cps | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.448 | |
| 3f3s | NAD | Lambda-crystallin homolog | / | 0.447 | |
| 4ng5 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.447 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.447 | |
| 1llu | NAD | Alcohol dehydrogenase | / | 0.446 | |
| 3ndr | NAD | Pyridoxal 4-dehydrogenase | 1.1.1.107 | 0.446 | |
| 3ruf | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.446 | |
| 4b8w | NAP | GDP-L-fucose synthase | 1.1.1.271 | 0.446 | |
| 2wdz | NAD | Galactitol dehydrogenase | / | 0.445 | |
| 2yy7 | NAD | L-threonine dehydrogenase | / | 0.445 | |
| 3a28 | NAD | L-2,3-butanediol dehydrogenase | 1.1.1.76 | 0.445 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.445 | |
| 4xq9 | NAD | Homospermidine synthase | 2.5.1.44 | 0.445 | |
| 5cds | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 1e3l | NAD | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.444 | |
| 1nyt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 1z7e | ATP | Bifunctional polymyxin resistance protein ArnA | / | 0.444 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.444 | |
| 3pef | NAP | Glyoxalate/3-oxopropanoate/4-oxobutanoate reductase | / | 0.444 | |
| 3doc | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.443 | |
| 1geg | NAD | Diacetyl reductase [(S)-acetoin forming] | 1.1.1.304 | 0.442 | |
| 1i3l | NAD | UDP-glucose 4-epimerase | / | 0.442 | |
| 1qor | NDP | Quinone oxidoreductase 1 | / | 0.442 | |
| 2rbe | NDP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.442 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.442 | |
| 4nd3 | NAD | Lactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase | / | 0.442 | |
| 4ros | APR | Malate dehydrogenase | / | 0.442 | |
| 4rvu | NDP | Probable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) | / | 0.442 | |
| 1w4z | NAP | Putative ketoacyl reductase | 1.3.1 | 0.441 | |
| 2vhz | NAI | Alanine dehydrogenase | 1.4.1.1 | 0.441 | |
| 3qw2 | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.441 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 1lde | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1wvg | APR | CDP-glucose 4,6-dehydratase | 4.2.1.45 | 0.440 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.440 | |
| 2zb3 | NDP | Prostaglandin reductase 2 | 1.3.1.48 | 0.440 | |
| 3ru9 | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 | |
| 3rue | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.440 |