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 |
|---|---|---|---|
| 1vhn | FMN | tRNA-dihydrouridine synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 1.252 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.956 | |
| 4yco | FMN | tRNA-dihydrouridine(16) synthase | / | 0.939 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.928 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.924 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.923 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.908 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.902 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.901 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.897 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.894 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.882 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.879 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.878 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.874 | |
| 4e2d | FMN | Dehydrogenase | / | 0.870 | |
| 3hf3 | FMN | Chromate reductase | / | 0.866 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.865 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.865 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.864 | |
| 2h8x | FMN | XenA | / | 0.863 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.862 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.859 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.856 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.852 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.847 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.845 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.845 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.845 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.843 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.842 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.833 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.832 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.831 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.830 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.830 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.824 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.821 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.814 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.814 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.813 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.811 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.809 | |
| 4jic | FMN | GTN Reductase | / | 0.808 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.805 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.805 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.801 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.800 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.800 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.799 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.798 | |
| 1gwj | FMN | Morphinone reductase | / | 0.796 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.790 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.789 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.789 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.788 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.787 | |
| 2zfa | FMN | Lactate oxidase | / | 0.783 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.783 | |
| 4cw5 | FMN | DfnA | / | 0.782 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.780 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.780 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.779 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.778 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.778 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.775 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.767 | |
| 1ofd | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.766 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.766 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.763 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.760 | |
| 4e2b | FMN | Dehydrogenase | / | 0.760 | |
| 4yx6 | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.757 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.755 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.755 | |
| 2j6x | FMN | Lactate oxidase | / | 0.754 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.754 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.750 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.748 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.747 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.745 | |
| 2nli | FMN | Lactate oxidase | / | 0.745 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.744 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.742 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.740 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.737 | |
| 4z38 | FMN | MlnA | / | 0.732 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.730 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.724 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.724 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.723 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.722 | |
| 5ebu | FMN | Lactate oxidase | / | 0.720 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.716 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.714 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.709 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.708 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.707 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.706 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.705 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.705 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.704 | |
| 2e77 | FMN | Lactate oxidase | / | 0.704 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.703 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.702 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.702 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.702 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.698 | |
| 1ep3 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.695 | |
| 1ych | FMN | Nitric oxide reductase | 1 | 0.695 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.694 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.690 | |
| 2du2 | FMN | Lactate oxidase | / | 0.690 | |
| 4m0c | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.687 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.684 | |
| 4rje | FNR | Lactate oxidase | / | 0.684 | |
| 2z9d | FMN | FMN-dependent NADH-azoreductase | / | 0.683 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.682 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.682 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.682 | |
| 4n9q | FMN | FMN-dependent NADH-azoreductase 1 | / | 0.682 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.681 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.679 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.678 | |
| 5a89 | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.678 | |
| 1ycg | FMN | Nitric oxide reductase | 1 | 0.676 | |
| 4j8p | FMN | Flavodoxin | / | 0.676 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.675 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.674 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 1ycf | FMN | Nitric oxide reductase | 1 | 0.673 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.672 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.672 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.670 | |
| 3n39 | FMN | Protein NrdI | / | 0.669 | |
| 1j8q | FMN | Flavodoxin | / | 0.668 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.667 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.667 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.667 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.666 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.665 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.665 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.663 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.662 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.662 | |
| 1t5b | FMN | FMN-dependent NADH-azoreductase | / | 0.661 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.661 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.661 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.660 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.660 | |
| 3klb | FMN | Uncharacterized protein | / | 0.660 | |
| 1zha | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.657 | |
| 1t8x | PEP | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.656 | |
| 3m12 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.656 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.656 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.655 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.654 | |
| 3bw3 | FMN | Putative 2-nitropropane dioxygenase | / | 0.654 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.654 | |
| 2fcr | FMN | Flavodoxin | / | 0.653 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.653 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.653 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.652 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.651 | |
| 3au2 | DGT | DNA polymerase beta family (X family) | / | 0.651 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.651 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.650 | |
| 2ohh | FMN | Type A flavoprotein FprA | 1 | 0.650 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.650 | |
| 3w77 | FMN | FMN-dependent NADH-azoreductase | / | 0.650 | |
| 4hs4 | FMN | Chromate reductase | / | 0.650 |