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 |
|---|---|---|---|
| 3p8j | FMN | Pentaerythritol tetranitrate reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 1.282 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 1.279 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 1.277 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 1.240 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 1.238 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 1.189 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 1.183 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 1.177 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 1.162 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 1.147 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 1.129 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 1.101 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 1.078 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.073 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 1.068 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 1.063 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.058 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 1.050 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.044 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 1.042 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.041 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 1.041 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 1.040 | |
| 4jic | FMN | GTN Reductase | / | 1.022 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 1.018 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.007 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 1.006 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 1.001 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.989 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.968 | |
| 4e2b | FMN | Dehydrogenase | / | 0.957 | |
| 4e2d | FMN | Dehydrogenase | / | 0.948 | |
| 1gwj | FMN | Morphinone reductase | / | 0.933 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.933 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.929 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.927 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.921 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.918 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.909 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.901 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.899 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.896 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.895 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.889 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.879 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.872 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.871 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.866 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.865 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.863 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.861 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.857 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.857 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.849 | |
| 2h8x | FMN | XenA | / | 0.843 | |
| 3hf3 | FMN | Chromate reductase | / | 0.842 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.842 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.840 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.839 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.837 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.837 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.825 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.825 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.821 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.820 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.811 | |
| 5ebu | FMN | Lactate oxidase | / | 0.810 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.809 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.804 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.804 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.804 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.799 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.798 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.789 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.785 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.778 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.778 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.766 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.760 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.759 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.755 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.754 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.754 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.749 | |
| 2nli | FMN | Lactate oxidase | / | 0.747 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.746 | |
| 4rje | FNR | Lactate oxidase | / | 0.745 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.743 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.742 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.740 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.738 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.735 | |
| 2zfa | FMN | Lactate oxidase | / | 0.731 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.731 | |
| 2j6x | FMN | Lactate oxidase | / | 0.730 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.729 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.729 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.728 | |
| 2du2 | FMN | Lactate oxidase | / | 0.717 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.714 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.713 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.712 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.707 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.705 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.704 | |
| 2e77 | FMN | Lactate oxidase | / | 0.695 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.694 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.691 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.685 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.682 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.681 | |
| 3esz | FMN | Flavodoxin | / | 0.680 | |
| 3n3b | FMN | Protein NrdI | / | 0.680 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.679 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.678 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.677 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.673 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.671 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.669 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.668 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.668 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.666 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.666 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.665 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.665 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.664 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.663 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.663 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.663 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.663 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.661 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.661 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.660 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.660 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.659 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.658 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.658 | |
| 5cho | FAD | Flavin reductase | / | 0.658 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.656 | |
| 4j8p | FMN | Flavodoxin | / | 0.656 | |
| 1t5b | FMN | FMN-dependent NADH-azoreductase | / | 0.654 | |
| 4z38 | FMN | MlnA | / | 0.653 | |
| 2cdu | FAD | NADH oxidase | / | 0.652 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.652 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.650 |