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 |
|---|---|---|---|
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 1.686 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 1.266 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 1.263 | |
| 3b03 | VNR | Isopentenyl-diphosphate delta-isomerase | / | 1.254 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 1.247 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 1.224 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 1.137 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 1.121 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 1.076 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.821 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.819 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.816 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.806 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.801 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.787 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.784 | |
| 2h8x | FMN | XenA | / | 0.771 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.764 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.758 | |
| 3hf3 | FMN | Chromate reductase | / | 0.755 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.750 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.749 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.743 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.742 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.739 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.737 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.736 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.735 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.735 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.734 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.730 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.727 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.726 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.722 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.721 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.720 | |
| 4bmo | FMN | Protein NrdI | / | 0.719 | |
| 1ea0 | FMN | Glutamate synthase [NADPH] large chain | 1.4.1.13 | 0.716 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.714 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.714 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.714 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.711 | |
| 2zfa | FMN | Lactate oxidase | / | 0.708 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.706 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.706 | |
| 2du2 | FMN | Lactate oxidase | / | 0.705 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.703 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.702 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.702 | |
| 3ojw | FMN | NADPH--cytochrome P450 reductase | / | 0.700 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.698 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.698 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.695 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.693 | |
| 1llz | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.686 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.684 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.684 | |
| 3n3b | FMN | Protein NrdI | / | 0.682 | |
| 2nli | FMN | Lactate oxidase | / | 0.678 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.676 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.675 | |
| 4rje | FNR | Lactate oxidase | / | 0.672 | |
| 2j6x | FMN | Lactate oxidase | / | 0.670 | |
| 4bmp | FMN | Protein NrdI | / | 0.669 | |
| 1t0i | FMN | NAD(P)H-dependent FMN reductase LOT6 | / | 0.668 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.667 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.666 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.665 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.662 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.662 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.661 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.660 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.660 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.656 | |
| 5ebu | FMN | Lactate oxidase | / | 0.656 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.655 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.654 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.654 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.652 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.651 | |
| 3qe2 | FMN | NADPH--cytochrome P450 reductase | / | 0.650 |