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 |
|---|---|---|---|
| 3lov | FAD | Protoporphyrinogen oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3lov | FAD | Protoporphyrinogen oxidase | / | 1.000 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.528 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.522 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.505 | |
| 1npt | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.487 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.487 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.485 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.485 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.485 | |
| 3ukl | FAD | UDP-galactopyranose mutase | / | 0.484 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.481 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.481 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.478 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.477 | |
| 2ohx | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.476 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.476 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.474 | |
| 3utg | FDA | UDP-galactopyranose mutase | / | 0.472 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.472 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.470 | |
| 3q8x | UD1 | Toxin zeta | / | 0.469 | |
| 3zc3 | NAP | Ferredoxin--NADP reductase | 1.18.1.2 | 0.469 | |
| 2bab | FAD | Putative aminooxidase | / | 0.468 | |
| 4u8p | FDA | UDP-galactopyranose mutase | / | 0.468 | |
| 5fl3 | ADP | Pili retraction protein PilT | / | 0.465 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.464 | |
| 4u8k | FDA | UDP-galactopyranose mutase | / | 0.463 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.461 | |
| 4tvb | NAD | Homospermidine synthase | 2.5.1.44 | 0.460 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.459 | |
| 1u28 | NAD | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.459 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.458 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.458 | |
| 1l7e | NAI | NAD(P) transhydrogenase subunit alpha part 1 | 1.6.1.2 | 0.457 | |
| 1p31 | EPU | UDP-N-acetylmuramate--L-alanine ligase | 6.3.2.8 | 0.457 | |
| 2jhf | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.457 | |
| 1a71 | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.455 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.455 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.454 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.453 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.453 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.453 | |
| 1mgo | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.452 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.452 | |
| 4fd2 | ADP | Chaperone protein ClpB | / | 0.452 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.452 | |
| 4nfh | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.452 | |
| 1kol | NAD | Glutathione-independent formaldehyde dehydrogenase | / | 0.451 | |
| 3ukk | FDA | UDP-galactopyranose mutase | / | 0.451 | |
| 4hfm | NAP | 2-alkenal reductase (NADP(+)-dependent) | / | 0.451 | |
| 4plp | NAD | Homospermidine synthase | 2.5.1.44 | 0.450 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.449 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.449 | |
| 4dwv | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.449 | |
| 4oag | ADP | Mitochondrial dynamics protein MID51 | / | 0.449 | |
| 3tnl | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.448 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.448 | |
| 4u8m | FDA | UDP-galactopyranose mutase | / | 0.448 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.447 | |
| 2bi7 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.446 | |
| 3wmx | NAD | NAD dependent epimerase/dehydratase | / | 0.446 | |
| 4ng5 | NAJ | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.446 | |
| 1hld | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.445 | |
| 3n7u | NAD | Formate dehydrogenase, chloroplastic/mitochondrial | / | 0.445 | |
| 4dpw | AGS | Mevalonate diphosphate decarboxylase | / | 0.445 | |
| 5cns | CDP | Ribonucleoside-diphosphate reductase 1 subunit alpha | 1.17.4.1 | 0.445 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.444 | |
| 3hwr | NDP | 2-dehydropantoate 2-reductase | / | 0.444 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.444 | |
| 5bsg | NAP | Pyrroline-5-carboxylate reductase | / | 0.444 | |
| 1c1d | NAI | Phenylalanine dehydrogenase | / | 0.443 | |
| 1glb | ADP | Glycerol kinase | / | 0.443 | |
| 2bjh | FER | Feruloyl esterase A | 3.1.1.73 | 0.443 | |
| 4rdi | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.443 | |
| 4u8l | FDA | UDP-galactopyranose mutase | / | 0.443 | |
| 2a4z | BYM | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.442 | |
| 2y3s | TIR | TamL | / | 0.442 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.442 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.442 | |
| 5jla | NAD | Putative short-chain dehydrogenase/reductase | / | 0.442 | |
| 1l3i | SAH | Probable cobalt-precorrin-6B C(15)-methyltransferase (decarboxylating) | / | 0.441 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.441 | |
| 2oxi | NAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.441 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.441 | |
| 2cmv | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.440 | |
| 2dbr | NAP | Glyoxylate reductase | 1.1.1.26 | 0.440 | |
| 3ssn | MVI | Mycinamicin VI 2''-O-methyltransferase | / | 0.440 | |
| 4l4s | NAI | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.440 | |
| 4w6z | 8ID | Alcohol dehydrogenase 1 | 1.1.1.1 | 0.440 |