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 |
|---|---|---|---|
| 5ebu | FMN | Lactate oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5ebu | FMN | Lactate oxidase | / | 1.356 | |
| 2du2 | FMN | Lactate oxidase | / | 1.253 | |
| 2j6x | FMN | Lactate oxidase | / | 1.208 | |
| 2e77 | FMN | Lactate oxidase | / | 1.093 | |
| 4rje | FNR | Lactate oxidase | / | 1.064 | |
| 2nli | FMN | Lactate oxidase | / | 1.056 | |
| 4yl2 | FMN | Lactate oxidase | / | 1.052 | |
| 2zfa | FMN | Lactate oxidase | / | 1.019 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.860 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.830 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.828 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.825 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.823 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.813 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.812 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.812 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.810 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.810 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.809 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.802 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.801 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.797 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.791 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.787 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.785 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.782 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.782 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.782 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.782 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.781 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.781 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.779 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.779 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.771 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.770 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.769 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.766 | |
| 4e2b | FMN | Dehydrogenase | / | 0.765 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.762 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.758 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.754 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.754 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.752 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.750 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.750 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.749 | |
| 3hf3 | FMN | Chromate reductase | / | 0.744 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.743 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.743 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.740 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.739 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.738 | |
| 1gwj | FMN | Morphinone reductase | / | 0.736 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.736 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.732 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.731 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.727 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.725 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.725 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.723 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.723 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.720 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.719 | |
| 2oz0 | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.718 | |
| 4e2d | FMN | Dehydrogenase | / | 0.717 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.711 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.710 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.709 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.708 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.707 | |
| 4jic | FMN | GTN Reductase | / | 0.705 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.700 | |
| 4nmc | FAD | Bifunctional protein PutA | / | 0.697 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.697 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.696 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.695 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.691 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.691 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.687 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.684 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.684 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.682 | |
| 4j8p | FMN | Flavodoxin | / | 0.681 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.680 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.680 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.680 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.678 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.677 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.677 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.676 | |
| 3oix | FMN | Dihydroorotate dehydrogenase | / | 0.675 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.673 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.673 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.673 | |
| 2fzm | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.671 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.671 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.669 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.666 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.666 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.665 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.663 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.662 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 2bi7 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.656 | |
| 2vxa | RBF | Dodecin | / | 0.656 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.656 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.656 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.655 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.655 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.655 | |
| 3umv | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.652 | |
| 1qcw | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.650 |