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 |
|---|---|---|---|
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 1.274 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 1.149 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 1.070 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.895 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.894 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.886 | |
| 1gwj | FMN | Morphinone reductase | / | 0.873 | |
| 2h8x | FMN | XenA | / | 0.871 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.869 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.865 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.864 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.862 | |
| 3hf3 | FMN | Chromate reductase | / | 0.859 | |
| 4e2d | FMN | Dehydrogenase | / | 0.850 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.839 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.838 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.838 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.836 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.834 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.829 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.828 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.826 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.826 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.821 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.821 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.818 | |
| 4e2b | FMN | Dehydrogenase | / | 0.808 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.808 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.808 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.799 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.798 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.797 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.797 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.796 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.796 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.792 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.789 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.789 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.788 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.787 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.786 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.777 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.772 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.770 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.766 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.763 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.760 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.758 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.755 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.755 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.753 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.750 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.749 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.748 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.747 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.746 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.743 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.742 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.741 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.739 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.737 | |
| 2du2 | FMN | Lactate oxidase | / | 0.736 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.734 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.732 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.730 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.730 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.729 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.728 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.727 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.724 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.711 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.711 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.711 | |
| 3n3b | FMN | Protein NrdI | / | 0.709 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.708 | |
| 2vyx | FMN | Dodecin | / | 0.707 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.703 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.701 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.698 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.697 | |
| 4rje | FNR | Lactate oxidase | / | 0.695 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.694 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.692 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.692 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.691 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.688 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.684 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.682 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.682 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.681 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.679 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.679 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.678 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.678 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.678 | |
| 2cdu | FAD | NADH oxidase | / | 0.677 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.676 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.676 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.676 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.676 | |
| 1zwl | FMN | NAD(P)H dehydrogenase (quinone) | 1.6.5.2 | 0.675 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.675 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.674 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.674 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.674 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.672 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.672 | |
| 2vxa | RBF | Dodecin | / | 0.672 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.671 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.669 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.669 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.669 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.668 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.667 | |
| 3lad | FAD | Dihydrolipoyl dehydrogenase | / | 0.667 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.666 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.665 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.664 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.663 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.663 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.663 | |
| 3klb | FMN | Uncharacterized protein | / | 0.663 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.663 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.663 | |
| 2g8d | UMP | Thymidylate synthase | / | 0.662 | |
| 2j09 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.662 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.662 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.662 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.662 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.662 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.661 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.660 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.660 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.660 | |
| 1ja1 | NAP | NADPH--cytochrome P450 reductase | / | 0.659 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.659 | |
| 4irr | UMP | Thymidylate synthase | / | 0.659 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.658 | |
| 4gi5 | FAD | Putative NAD(P)H dehydrogenase (Quinone) | / | 0.658 | |
| 4jic | FMN | GTN Reductase | / | 0.658 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.657 | |
| 4cw5 | FMN | DfnA | / | 0.657 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.657 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.655 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.655 | |
| 1np7 | FAD | Cryptochrome DASH | / | 0.654 | |
| 1q1w | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.654 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.654 | |
| 3qj7 | UMP | Thymidylate synthase ThyA | / | 0.654 | |
| 1lvg | 5GP | Guanylate kinase | 2.7.4.8 | 0.653 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.653 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.653 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.652 | |
| 1fnd | A2P | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.651 | |
| 2nli | FMN | Lactate oxidase | / | 0.651 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.651 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.650 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.650 |