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 |
|---|---|---|---|
| 3n19 | FNR | Xenobiotic reductase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3n19 | FNR | Xenobiotic reductase | / | 1.373 | |
| 4utk | FNR | Xenobiotic reductase | / | 1.325 | |
| 4utl | FNR | Xenobiotic reductase | / | 1.219 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 1.203 | |
| 3l67 | FMN | Xenobiotic reductase | / | 1.149 | |
| 4uth | FMN | Xenobiotic reductase | / | 1.139 | |
| 4utm | FNR | Xenobiotic reductase | / | 1.139 | |
| 3l5l | FMN | Xenobiotic reductase | / | 1.138 | |
| 2h8x | FMN | XenA | / | 1.113 | |
| 3n14 | FMN | Xenobiotic reductase | / | 1.074 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 1.028 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.933 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.927 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.927 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.924 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.921 | |
| 4jic | FMN | GTN Reductase | / | 0.917 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.913 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.908 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.904 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.901 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.893 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.893 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.890 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.888 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.877 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.875 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.875 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.875 | |
| 2zfa | FMN | Lactate oxidase | / | 0.874 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.874 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.873 | |
| 4e2d | FMN | Dehydrogenase | / | 0.872 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.865 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.861 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.861 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.860 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.859 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.858 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.858 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.854 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.852 | |
| 4e2b | FMN | Dehydrogenase | / | 0.849 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.847 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.843 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.840 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.834 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.830 | |
| 2nli | FMN | Lactate oxidase | / | 0.824 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.821 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.820 | |
| 1gwj | FMN | Morphinone reductase | / | 0.818 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.814 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.811 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.808 | |
| 2j6x | FMN | Lactate oxidase | / | 0.805 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.805 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.797 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.789 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.787 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.785 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.785 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.784 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.783 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.782 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.782 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.780 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.774 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.772 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.770 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.768 | |
| 4wzh | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.767 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.765 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.764 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.762 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.762 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.758 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.754 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.753 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.751 | |
| 2z6i | FMN | 2-nitropropane dioxygenase | / | 0.750 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.745 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.744 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.741 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.739 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.738 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.731 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.724 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.719 | |
| 1ofe | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.718 | |
| 3hf3 | FMN | Chromate reductase | / | 0.714 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.713 | |
| 4cw5 | FMN | DfnA | / | 0.713 | |
| 4ef9 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.711 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.707 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.705 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.703 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.702 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.702 | |
| 1llw | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.699 | |
| 4hnb | FMN | LOV protein | / | 0.697 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.695 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.690 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.688 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.686 | |
| 2vi5 | Y19 | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.685 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.684 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.681 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.679 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.679 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.676 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.673 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.672 | |
| 2ohh | FMN | Type A flavoprotein FprA | 1 | 0.671 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.670 | |
| 4z38 | FMN | MlnA | / | 0.670 | |
| 2vyx | FMN | Dodecin | / | 0.669 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.666 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.666 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.665 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.665 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.662 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.660 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.660 | |
| 3n3a | FMN | Protein NrdI | / | 0.659 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.659 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.658 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.656 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.655 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.655 | |
| 1ycf | FMN | Nitric oxide reductase | 1 | 0.654 | |
| 4bmo | FMN | Protein NrdI | / | 0.653 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.652 | |
| 3w8w | FAD | Putative FAD-dependent oxygenase EncM | / | 0.651 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.650 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.650 |