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 |
|---|---|---|---|
| 2z6i | FMN | 2-nitropropane dioxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 1.283 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 1.017 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.857 | |
| 1ofe | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.833 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.831 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.828 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.820 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.811 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.811 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.810 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.810 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.803 | |
| 1llz | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.792 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.791 | |
| 4rje | FNR | Lactate oxidase | / | 0.788 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.787 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.787 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.786 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.785 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.778 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.777 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.777 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.775 | |
| 5ebu | FMN | Lactate oxidase | / | 0.766 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.765 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.765 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.765 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.764 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.763 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.761 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.759 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.758 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.757 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.756 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.756 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.755 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.751 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.750 | |
| 4e2d | FMN | Dehydrogenase | / | 0.749 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.747 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.746 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.745 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.745 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.743 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.743 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.742 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.741 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.741 | |
| 2h8x | FMN | XenA | / | 0.740 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.739 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.738 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.737 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.735 | |
| 2j6x | FMN | Lactate oxidase | / | 0.735 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.734 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.732 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.731 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.730 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.730 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.729 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.729 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.729 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.728 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.728 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.727 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.725 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.725 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.725 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.725 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.723 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.722 | |
| 3hf3 | FMN | Chromate reductase | / | 0.718 | |
| 2zfa | FMN | Lactate oxidase | / | 0.716 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.715 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.714 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.712 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.710 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.708 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.708 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.707 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.705 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.704 | |
| 4jic | FMN | GTN Reductase | / | 0.704 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.702 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.702 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.702 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.693 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.691 | |
| 4cw5 | FMN | DfnA | / | 0.690 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.688 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.683 | |
| 1k8y | 13P | Tryptophan synthase alpha chain | / | 0.682 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.680 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.677 | |
| 2du2 | FMN | Lactate oxidase | / | 0.676 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.676 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.675 | |
| 1qcw | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.674 | |
| 2e77 | FMN | Lactate oxidase | / | 0.674 | |
| 1t0i | FMN | NAD(P)H-dependent FMN reductase LOT6 | / | 0.673 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.670 | |
| 3fsu | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.669 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.669 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.669 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.668 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.668 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.668 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.668 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.666 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.666 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.665 | |
| 1iqr | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.664 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.664 | |
| 4e2b | FMN | Dehydrogenase | / | 0.664 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.663 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.663 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.662 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.661 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.661 | |
| 5dkk | FMN | Predicted protein | / | 0.661 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.660 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.659 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.658 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.657 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.656 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.655 | |
| 3esz | FMN | Flavodoxin | / | 0.654 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.651 | |
| 1owo | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.650 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.650 | |
| 3n39 | FMN | Protein NrdI | / | 0.650 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.650 |