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 |
|---|---|---|---|
| 2nli | FMN | Lactate oxidase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2nli | FMN | Lactate oxidase | / | 1.384 | |
| 2zfa | FMN | Lactate oxidase | / | 1.344 | |
| 4yl2 | FMN | Lactate oxidase | / | 1.263 | |
| 2j6x | FMN | Lactate oxidase | / | 1.255 | |
| 4rje | FNR | Lactate oxidase | / | 1.213 | |
| 2e77 | FMN | Lactate oxidase | / | 1.170 | |
| 5ebu | FMN | Lactate oxidase | / | 1.056 | |
| 2du2 | FMN | Lactate oxidase | / | 1.027 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.991 | |
| 1szf | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.927 | |
| 1fcb | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.904 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.895 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.871 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.856 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.839 | |
| 2oz0 | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.839 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.838 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.838 | |
| 3n14 | FMN | Xenobiotic reductase | / | 0.838 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.836 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.836 | |
| 2h8x | FMN | XenA | / | 0.829 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.825 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.824 | |
| 4utm | FNR | Xenobiotic reductase | / | 0.822 | |
| 4utl | FNR | Xenobiotic reductase | / | 0.819 | |
| 4iql | FMN | Enoyl-(Acyl-carrier-protein) reductase II | / | 0.818 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.816 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.816 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.815 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.814 | |
| 4e2d | FMN | Dehydrogenase | / | 0.801 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.799 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.790 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.786 | |
| 4jic | FMN | GTN Reductase | / | 0.783 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.781 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.781 | |
| 1k02 | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.774 | |
| 5cpm | FNR | NADH:flavin oxidoreductase | / | 0.770 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.765 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.763 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.763 | |
| 3gr8 | FMN | NADPH dehydrogenase | / | 0.762 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.760 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.753 | |
| 1qcw | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.748 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.747 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.745 | |
| 3hf3 | FMN | Chromate reductase | / | 0.733 | |
| 1gwj | FMN | Morphinone reductase | / | 0.732 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.732 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.728 | |
| 3gye | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.728 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.726 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.723 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.722 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.716 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.714 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.710 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.708 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.707 | |
| 2djx | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.705 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.695 | |
| 2djl | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.691 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.690 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.690 | |
| 4cw5 | FMN | DfnA | / | 0.690 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.687 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.687 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.686 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.686 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.683 | |
| 4e2b | FMN | Dehydrogenase | / | 0.682 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.681 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.680 | |
| 4j8p | FMN | Flavodoxin | / | 0.680 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.679 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.678 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.677 | |
| 1wsb | FMN | Flavodoxin | / | 0.676 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.676 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.676 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.674 | |
| 3lcu | SAH | 16S rRNA (guanine(1405)-N(7))-methyltransferase | 2.1.1.179 | 0.673 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.672 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.672 | |
| 1u4s | BIH | L-lactate dehydrogenase | 1.1.1.27 | 0.672 | |
| 2a58 | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.671 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.671 | |
| 4h4y | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.670 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.669 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.669 | |
| 2bsl | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.668 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.668 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.667 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.666 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.665 | |
| 1b5t | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.664 | |
| 3icr | COA | Coenzyme A disulfide reductase | / | 0.664 | |
| 4df4 | 0L3 | DNA polymerase I, thermostable | 2.7.7.7 | 0.664 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.663 | |
| 3e78 | TPP | High affinity transport system protein p37 | / | 0.663 | |
| 1szg | FNS | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.662 | |
| 3t0i | SAH | Putative methyltransferase | / | 0.662 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.661 | |
| 3vkj | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.661 | |
| 2vyx | FMN | Dodecin | / | 0.660 | |
| 1eje | FMN | Protein MTH_152 | / | 0.657 | |
| 1u5a | BIK | L-lactate dehydrogenase | 1.1.1.27 | 0.657 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.657 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.657 | |
| 4emy | PLP | Aminotransferase class I and II | / | 0.657 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.657 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.656 | |
| 4gu5 | FAD | Cryptochrome-1 | / | 0.656 | |
| 4h4w | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.656 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.656 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.655 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.655 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.655 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.654 | |
| 4ef8 | FMN | Dihydroorotate dehydrogenase (fumarate) | / | 0.654 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.653 | |
| 1ao0 | 5GP | Amidophosphoribosyltransferase | / | 0.651 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.651 | |
| 4bf9 | FMN | tRNA-dihydrouridine(16) synthase | / | 0.651 | |
| 4y7c | FMN | NADPH--cytochrome P450 reductase | / | 0.651 | |
| 1nb9 | RBF | Riboflavin kinase | 2.7.1.26 | 0.650 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.650 |