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 |
|---|---|---|---|
| 4yco | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 1.276 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 1.149 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 1.047 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.942 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.939 | |
| 2h8x | FMN | XenA | / | 0.936 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.934 | |
| 4jic | FMN | GTN Reductase | / | 0.934 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.919 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.916 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.915 | |
| 3hf3 | FMN | Chromate reductase | / | 0.910 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.905 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.883 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.876 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.876 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.874 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.873 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.873 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.870 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.868 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.866 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.864 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.863 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.861 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.859 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.857 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.856 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.855 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.855 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.851 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.847 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.847 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.846 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.844 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.842 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.841 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.840 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.839 | |
| 4e2b | FMN | Dehydrogenase | / | 0.833 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.828 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.827 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.825 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.824 | |
| 4e2d | FMN | Dehydrogenase | / | 0.822 | |
| 1gwj | FMN | Morphinone reductase | / | 0.819 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.818 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.814 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.814 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.810 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.809 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.806 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.803 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.799 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.796 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.790 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.787 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.787 | |
| 5ebu | FMN | Lactate oxidase | / | 0.779 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.769 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.768 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.762 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.762 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.762 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.762 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.755 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.750 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.747 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.745 | |
| 2j6x | FMN | Lactate oxidase | / | 0.744 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.744 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.743 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.741 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.735 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.735 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.732 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.730 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.730 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.729 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.728 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.725 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.723 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.722 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.722 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.716 | |
| 4cw5 | FMN | DfnA | / | 0.715 | |
| 2e77 | FMN | Lactate oxidase | / | 0.714 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.712 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.711 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.711 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.710 | |
| 2du2 | FMN | Lactate oxidase | / | 0.707 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.702 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.700 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.700 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.700 | |
| 2nli | FMN | Lactate oxidase | / | 0.697 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.695 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.694 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.691 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.691 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.686 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.685 | |
| 4j8p | FMN | Flavodoxin | / | 0.685 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.683 | |
| 3n3b | FMN | Protein NrdI | / | 0.683 | |
| 4jzy | FAD | Cryptochrome-1 | / | 0.683 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.682 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.680 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.679 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.677 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.677 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.677 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.677 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.676 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.676 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.675 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.675 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.673 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.672 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.672 | |
| 3bw4 | FMN | Putative 2-nitropropane dioxygenase | / | 0.671 | |
| 4gu5 | FAD | Cryptochrome-1 | / | 0.671 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.671 | |
| 3klb | FMN | Uncharacterized protein | / | 0.670 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.669 | |
| 1gxf | FAD | Trypanothione reductase | 1.8.1.12 | 0.669 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.668 | |
| 4brg | GNP | Ectonucleoside triphosphate diphosphohydrolase I | / | 0.665 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.663 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.663 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.663 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.662 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.662 | |
| 2vyx | FMN | Dodecin | / | 0.662 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.662 | |
| 1ofv | FMN | Flavodoxin | / | 0.661 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.661 | |
| 4irr | UMP | Thymidylate synthase | / | 0.660 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.659 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.658 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.658 | |
| 1ndc | TYD | Nucleoside diphosphate kinase, cytosolic | 2.7.4.6 | 0.657 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.657 | |
| 3n39 | FMN | Protein NrdI | / | 0.657 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.655 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.653 | |
| 4kto | FAD | Putative isovaleryl-CoA dehydrogenase protein | / | 0.653 | |
| 4nev | FAD | Trypanothione reductase | / | 0.653 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.653 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.652 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.652 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.651 | |
| 3f90 | FMN | Flavodoxin | / | 0.651 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.651 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.650 | |
| 2j09 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.650 |