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 |
|---|---|---|---|
| 4yl2 | FMN | Lactate oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4yl2 | FMN | Lactate oxidase | / | 1.378 | |
| 2j6x | FMN | Lactate oxidase | / | 1.292 | |
| 2nli | FMN | Lactate oxidase | / | 1.263 | |
| 4rje | FNR | Lactate oxidase | / | 1.258 | |
| 2zfa | FMN | Lactate oxidase | / | 1.229 | |
| 2e77 | FMN | Lactate oxidase | / | 1.204 | |
| 5ebu | FMN | Lactate oxidase | / | 1.052 | |
| 2du2 | FMN | Lactate oxidase | / | 1.036 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.984 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.917 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.914 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.912 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.895 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.840 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.837 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.836 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.825 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.807 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.805 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.805 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.804 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.796 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.794 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.793 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.792 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.792 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.789 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.789 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.787 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.786 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.781 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.779 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.778 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.772 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.772 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.764 | |
| 1qcw | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.763 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.762 | |
| 4e2b | FMN | Dehydrogenase | / | 0.762 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.757 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.756 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.755 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.751 | |
| 2oz0 | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.749 | |
| 1gwj | FMN | Morphinone reductase | / | 0.746 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.745 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.742 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.741 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.740 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.739 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.738 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.734 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.731 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.731 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.726 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.723 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.723 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.717 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.715 | |
| 2h8x | FMN | XenA | / | 0.711 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.711 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.711 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.706 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.706 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.705 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.704 | |
| 3hf3 | FMN | Chromate reductase | / | 0.702 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.700 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.698 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.694 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.694 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.692 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.691 | |
| 4h4p | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.691 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.691 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.691 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.690 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.690 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.689 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.686 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.686 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.685 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.685 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.683 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.682 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.682 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.680 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.680 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.678 | |
| 4df4 | 0L3 | DNA polymerase I, thermostable | 2.7.7.7 | 0.677 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.677 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.676 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.675 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.675 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.675 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 1x31 | FMN | Subunit alpha of sarocosine oxidase | / | 0.674 | |
| 1x31 | FMN | Subunit beta of sarcosine oxidase | / | 0.674 | |
| 1vrq | FMN | Subunit alpha of sarocosine oxidase | / | 0.673 | |
| 1vrq | FMN | Subunit beta of sarcosine oxidase | / | 0.673 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.672 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.670 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.670 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.670 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.670 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.670 | |
| 1p4m | FMN | Riboflavin kinase | 2.7.1.26 | 0.669 | |
| 4j8p | FMN | Flavodoxin | / | 0.668 | |
| 1usc | FMN | Monooxygenase | / | 0.666 | |
| 4hia | FMN | LOV protein | / | 0.665 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.665 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.663 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.663 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.662 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.662 | |
| 3e78 | TPP | High affinity transport system protein p37 | / | 0.662 | |
| 5ayz | NCN | Nicotinate-nucleotide pyrophosphorylase [carboxylating] | 2.4.2.19 | 0.662 | |
| 4dfk | 0L5 | DNA polymerase I, thermostable | 2.7.7.7 | 0.660 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.656 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.656 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.656 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.655 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.655 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.655 | |
| 1nb9 | RBF | Riboflavin kinase | 2.7.1.26 | 0.654 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.654 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.654 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.654 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.654 | |
| 4h6p | FMN | Chromate reductase | / | 0.654 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.653 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.653 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.653 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.652 | |
| 4hut | ATP | Cob(I)yrinic acid a,c-diamide adenosyltransferase | 2.5.1.17 | 0.651 | |
| 4n65 | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.651 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.650 |