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 |
|---|---|---|---|
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 1.300 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 1.113 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 1.087 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 1.057 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 1.047 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.998 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.937 | |
| 4jic | FMN | GTN Reductase | / | 0.929 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.920 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.918 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.912 | |
| 2h8x | FMN | XenA | / | 0.912 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.906 | |
| 4e2b | FMN | Dehydrogenase | / | 0.904 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.902 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.900 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.896 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.894 | |
| 4e2d | FMN | Dehydrogenase | / | 0.892 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.888 | |
| 3hf3 | FMN | Chromate reductase | / | 0.882 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.873 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.869 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.868 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.866 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.865 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.862 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.861 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.859 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.856 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.855 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.846 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.846 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.844 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.842 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.841 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.839 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.835 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.833 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.832 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.831 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.828 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.828 | |
| 5ebu | FMN | Lactate oxidase | / | 0.828 | |
| 1gwj | FMN | Morphinone reductase | / | 0.827 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.820 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.818 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.818 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.815 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.813 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.812 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.810 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.809 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.809 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.806 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.804 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.802 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.801 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.799 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.798 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.796 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.793 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.793 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.793 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.792 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.792 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.785 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.782 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.781 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.776 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.775 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.774 | |
| 2j6x | FMN | Lactate oxidase | / | 0.772 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.768 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.762 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.761 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.761 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.760 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.760 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.760 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.750 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.747 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.745 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.744 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.743 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.743 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.740 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.739 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.739 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.738 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.735 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.735 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.733 | |
| 4cw5 | FMN | DfnA | / | 0.723 | |
| 4z38 | FMN | MlnA | / | 0.721 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.720 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.715 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.710 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.710 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.709 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.707 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.707 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.707 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.704 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.704 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.702 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.702 | |
| 2e77 | FMN | Lactate oxidase | / | 0.700 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.699 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.698 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.694 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.693 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.690 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.689 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.688 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.687 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.685 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.685 | |
| 2du2 | FMN | Lactate oxidase | / | 0.684 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.683 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.683 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.680 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.678 | |
| 1qcw | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.677 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.676 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.676 | |
| 1r2j | FAD | FkbI | / | 0.675 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.674 | |
| 1ofe | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.674 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.674 | |
| 4rje | FNR | Lactate oxidase | / | 0.674 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.673 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.672 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.671 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.671 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.670 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.670 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.670 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.668 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.667 | |
| 1ofv | FMN | Flavodoxin | / | 0.665 | |
| 1p4m | FMN | Riboflavin kinase | 2.7.1.26 | 0.665 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.665 | |
| 3esz | FMN | Flavodoxin | / | 0.665 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.665 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.665 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.663 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.663 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.661 | |
| 1akw | FMN | Flavodoxin | / | 0.660 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.660 | |
| 1llz | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.659 | |
| 4eb4 | UMP | Thymidylate synthase | 2.1.1.45 | 0.659 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.659 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.658 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.658 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.657 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.656 | |
| 3fsu | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.656 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.655 | |
| 2vxa | RBF | Dodecin | / | 0.655 | |
| 4hs4 | FMN | Chromate reductase | / | 0.655 | |
| 1owp | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.654 | |
| 2fcr | FMN | Flavodoxin | / | 0.654 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.654 | |
| 3f6r | FMN | Flavodoxin | / | 0.653 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.652 | |
| 1czn | FMN | Flavodoxin | / | 0.651 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.651 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.651 | |
| 5bnt | NAP | Aspartate-semialdehyde dehydrogenase | 1.2.1.11 | 0.651 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.650 | |
| 1yrx | FMN | AppA protein | / | 0.650 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.650 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.650 |