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 |
|---|---|---|---|
| 5af7 | FAD | Acyl-CoA dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 1.549 | |
| 5ahs | FAD | Acyl-CoA dehydrogenase | / | 1.083 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 1.075 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 1.000 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.998 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.968 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.939 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.932 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.909 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.907 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.906 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.891 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.885 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.884 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.876 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.875 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.859 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.836 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.829 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.829 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.820 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.811 | |
| 1r2j | FAD | FkbI | / | 0.802 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.797 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.792 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.777 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.775 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.774 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.771 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.771 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.769 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.760 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.750 | |
| 4kto | FAD | Putative isovaleryl-CoA dehydrogenase protein | / | 0.750 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.733 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.730 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.729 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.725 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.724 | |
| 4hj6 | FMN | LOV protein | / | 0.712 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.709 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.705 | |
| 4irn | FAD | AnaB | / | 0.700 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.699 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.698 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.696 | |
| 3rh7 | FMN | Uncharacterized protein | / | 0.696 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.693 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.692 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.692 | |
| 5j4e | FMN | Sensory box protein | / | 0.691 | |
| 1gaq | FAD | Ferredoxin | / | 0.688 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.686 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.684 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.684 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.684 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.682 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.681 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.681 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.679 | |
| 5a89 | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.679 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.676 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.675 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.674 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.672 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.671 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.670 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.669 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.669 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.666 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.666 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.665 | |
| 4jay | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.665 | |
| 4hj4 | FMN | LOV protein | / | 0.664 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.663 | |
| 5cho | FAD | Flavin reductase | / | 0.663 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.662 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.662 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.661 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.660 | |
| 1akw | FMN | Flavodoxin | / | 0.659 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.659 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.658 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.658 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.658 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.658 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.657 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.657 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.656 | |
| 4hia | FMN | LOV protein | / | 0.656 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.655 | |
| 4xoo | FMN | Coenzyme F420:L-glutamate ligase | / | 0.655 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.654 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.654 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.653 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 4wf0 | FMN | NPH1-1 | / | 0.652 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.651 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.651 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.651 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.651 |