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 |
|---|---|---|---|
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.274 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.265 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.183 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.169 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.118 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.118 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.114 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.103 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.093 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 1.061 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 1.004 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.994 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.989 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.984 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.975 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.955 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.939 | |
| 1qr2 | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.929 | |
| 4gi5 | FAD | Putative NAD(P)H dehydrogenase (Quinone) | / | 0.849 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.846 | |
| 4j8p | FMN | Flavodoxin | / | 0.790 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.763 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.761 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.739 | |
| 3klb | FMN | Uncharacterized protein | / | 0.734 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.732 | |
| 3lcm | FAD | Putative oxidoreductase | / | 0.731 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.726 | |
| 1t5b | FMN | FMN-dependent NADH-azoreductase | / | 0.725 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.724 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.721 | |
| 1zwl | FMN | NAD(P)H dehydrogenase (quinone) | 1.6.5.2 | 0.716 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.712 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.711 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.710 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.709 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.709 | |
| 1gwj | FMN | Morphinone reductase | / | 0.707 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.707 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.706 | |
| 4jic | FMN | GTN Reductase | / | 0.706 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.706 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.706 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.705 | |
| 2r97 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.703 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.703 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.701 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.699 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.699 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.699 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.699 | |
| 3zho | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.698 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.698 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.698 | |
| 4dy4 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.697 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.695 | |
| 4e2d | FMN | Dehydrogenase | / | 0.695 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.694 | |
| 3b03 | VNR | Isopentenyl-diphosphate delta-isomerase | / | 0.693 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.693 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.692 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.692 | |
| 1p0n | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.691 | |
| 2h8x | FMN | XenA | / | 0.691 | |
| 4cw5 | FMN | DfnA | / | 0.690 | |
| 4hs4 | FMN | Chromate reductase | / | 0.690 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.687 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.685 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.685 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.682 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.680 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.679 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.678 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.677 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.676 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.676 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.674 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.674 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.673 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.672 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.671 | |
| 4aut | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.671 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.670 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.670 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.670 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.670 | |
| 2r96 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.669 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.669 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.669 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.668 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.668 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.668 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.667 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.667 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.666 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.666 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.666 | |
| 1azl | FMN | Flavodoxin | / | 0.665 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.664 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.664 | |
| 5f12 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.664 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.663 | |
| 3n3b | FMN | Protein NrdI | / | 0.663 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.662 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.662 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.662 | |
| 4e2b | FMN | Dehydrogenase | / | 0.662 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.662 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.661 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.661 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.660 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.660 | |
| 1akw | FMN | Flavodoxin | / | 0.659 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.659 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.659 | |
| 2e77 | FMN | Lactate oxidase | / | 0.659 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.659 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.659 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.659 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.659 | |
| 1akr | FMN | Flavodoxin | / | 0.658 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.658 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.658 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.657 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.657 | |
| 4l82 | FMN | Uncharacterized protein | / | 0.656 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.655 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.655 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.655 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.654 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.654 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.654 | |
| 4bmp | FMN | Protein NrdI | / | 0.654 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.654 | |
| 1yqz | FAD | Coenzyme A disulfide reductase | / | 0.653 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.653 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.652 | |
| 3n39 | FMN | Protein NrdI | / | 0.652 |