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 |
|---|---|---|---|
| 4utm | FNR | Xenobiotic reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4utm | FNR | Xenobiotic reductase | / | 1.253 | |
| 4uth | FMN | Xenobiotic reductase | / | 1.250 | |
| 3l5l | FMN | Xenobiotic reductase | / | 1.234 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 1.227 | |
| 3l67 | FMN | Xenobiotic reductase | / | 1.226 | |
| 4utk | FNR | Xenobiotic reductase | / | 1.206 | |
| 2h8x | FMN | XenA | / | 1.182 | |
| 3n14 | FMN | Xenobiotic reductase | / | 1.167 | |
| 4utl | FNR | Xenobiotic reductase | / | 1.152 | |
| 3n19 | FNR | Xenobiotic reductase | / | 1.139 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 1.078 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 1.048 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 1.023 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 1.018 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 1.012 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 1.000 | |
| 3hf3 | FMN | Chromate reductase | / | 0.978 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.978 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.977 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.972 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.972 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.962 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.955 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.952 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.950 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.949 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.943 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.934 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.933 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.933 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.926 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.923 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.921 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.920 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.919 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.918 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.917 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.913 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.906 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.906 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.900 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.897 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.892 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.889 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.889 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.884 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.877 | |
| 4e2d | FMN | Dehydrogenase | / | 0.877 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.874 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.873 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.871 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.869 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.867 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.866 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.864 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.862 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.858 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.857 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.856 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.855 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.853 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.848 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.844 | |
| 1gwj | FMN | Morphinone reductase | / | 0.843 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.842 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.841 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.838 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.837 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.833 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.832 | |
| 2zfa | FMN | Lactate oxidase | / | 0.832 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.831 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.829 | |
| 4jic | FMN | GTN Reductase | / | 0.828 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.826 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.824 | |
| 2nli | FMN | Lactate oxidase | / | 0.822 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.822 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.816 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.815 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.815 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.806 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.805 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.804 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.801 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.800 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.789 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.783 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.781 | |
| 2j6x | FMN | Lactate oxidase | / | 0.780 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.773 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.772 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.770 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.767 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.763 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.752 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.749 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.749 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.748 | |
| 1ofe | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.747 | |
| 2e77 | FMN | Lactate oxidase | / | 0.745 | |
| 4cw5 | FMN | DfnA | / | 0.742 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.741 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.739 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.736 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.729 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.727 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.726 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.722 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.720 | |
| 2du2 | FMN | Lactate oxidase | / | 0.719 | |
| 4rje | FNR | Lactate oxidase | / | 0.718 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.712 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.711 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.696 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.693 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.692 | |
| 5ebu | FMN | Lactate oxidase | / | 0.691 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.690 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.690 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.689 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.686 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.684 | |
| 1llz | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.683 | |
| 4hnb | FMN | LOV protein | / | 0.681 | |
| 4z38 | FMN | MlnA | / | 0.678 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.677 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.675 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.675 | |
| 2g86 | UMP | Thymidylate synthase | / | 0.673 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.672 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.669 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.669 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.668 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.667 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.667 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.661 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.661 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.660 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.660 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.660 | |
| 4j8p | FMN | Flavodoxin | / | 0.659 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.659 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.658 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.657 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.657 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.655 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.655 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.655 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.653 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.653 | |
| 2vxa | RBF | Dodecin | / | 0.652 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.650 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.650 | |
| 2vyx | FMN | Dodecin | / | 0.650 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.650 |