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 |
|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 1.262 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 1.070 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 1.047 | |
| 2h8x | FMN | XenA | / | 0.949 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.942 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.925 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.923 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.918 | |
| 3hf3 | FMN | Chromate reductase | / | 0.907 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.904 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.903 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.897 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.894 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.885 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.884 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.883 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.878 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.878 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.873 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.861 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.861 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.858 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.857 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.856 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.853 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.850 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.849 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.848 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.847 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.845 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.844 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.840 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.839 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.839 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.833 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.831 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.830 | |
| 4e2d | FMN | Dehydrogenase | / | 0.820 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.819 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.818 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.811 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.808 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.808 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.807 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.807 | |
| 4e2b | FMN | Dehydrogenase | / | 0.805 | |
| 1gwj | FMN | Morphinone reductase | / | 0.801 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.801 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.800 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.795 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.793 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.788 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.788 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.786 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.784 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.778 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.777 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.766 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.762 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.762 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.762 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.759 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.757 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.756 | |
| 5ebu | FMN | Lactate oxidase | / | 0.754 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.753 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.751 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.747 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.744 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.744 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.744 | |
| 2j6x | FMN | Lactate oxidase | / | 0.741 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.739 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.738 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.738 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.736 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.734 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.732 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.731 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.731 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.725 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.724 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.724 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.720 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.720 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.718 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.718 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.717 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.716 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.715 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.715 | |
| 2e77 | FMN | Lactate oxidase | / | 0.710 | |
| 4z38 | FMN | MlnA | / | 0.710 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.709 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.708 | |
| 2du2 | FMN | Lactate oxidase | / | 0.707 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.705 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.704 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.704 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.699 | |
| 4rje | FNR | Lactate oxidase | / | 0.696 | |
| 3esz | FMN | Flavodoxin | / | 0.695 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.694 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.693 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.692 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.692 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.689 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.688 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.687 | |
| 3n3b | FMN | Protein NrdI | / | 0.687 | |
| 4irr | UMP | Thymidylate synthase | / | 0.686 | |
| 4a1o | AMZ | Bifunctional purine biosynthesis protein PurH | 2.1.2.3 | 0.682 | |
| 3bw2 | FMN | Putative 2-nitropropane dioxygenase | / | 0.681 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.681 | |
| 3zxs | FAD | Deoxyribodipyrimidine photolyase-related protein | / | 0.680 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.679 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.678 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 4nev | FAD | Trypanothione reductase | / | 0.674 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.673 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.672 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.672 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.671 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.670 | |
| 4gu5 | FAD | Cryptochrome-1 | / | 0.670 | |
| 1llz | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.668 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.668 | |
| 1f06 | NDP | Meso-diaminopimelate D-dehydrogenase | 1.4.1.16 | 0.667 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.665 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.665 | |
| 1ofv | FMN | Flavodoxin | / | 0.662 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.662 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.661 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.660 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.660 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.659 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.659 | |
| 1czn | FMN | Flavodoxin | / | 0.658 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.658 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.658 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.656 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.656 | |
| 4q4k | FMN | Uncharacterized protein | / | 0.656 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.655 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.654 | |
| 3qj7 | UMP | Thymidylate synthase ThyA | / | 0.654 | |
| 1tj0 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.653 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.653 | |
| 2j08 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.651 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.651 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.650 |