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 Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 1.390 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.834 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.805 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.803 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.770 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.762 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.748 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.744 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.743 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.722 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.715 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.714 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.713 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.711 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.701 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.701 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.700 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.700 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.696 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.696 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.694 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.692 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.692 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.690 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.690 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.684 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.680 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.678 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.677 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.677 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.676 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.676 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.675 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.674 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.674 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.673 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.668 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.667 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.667 | |
| 3qj4 | FAD | Renalase | / | 0.666 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.666 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.666 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.665 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.664 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.664 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.664 | |
| 4ysh | FAD | Glycine oxidase | / | 0.664 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.663 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.663 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.663 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.662 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.662 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.662 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.662 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.662 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.661 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.661 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.660 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.659 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.659 | |
| 4u8l | FDA | UDP-galactopyranose mutase | / | 0.659 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.658 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.657 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.657 | |
| 2bab | FAD | Putative aminooxidase | / | 0.656 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.656 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.655 | |
| 2c31 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.655 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.655 | |
| 3rh7 | FMN | Uncharacterized protein | / | 0.655 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.655 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.655 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.655 | |
| 2bac | FAD | Putative aminooxidase | / | 0.653 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.652 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.652 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.651 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.651 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.651 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.650 |