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 |
|---|---|---|---|
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.288 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.091 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.083 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.828 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.825 | |
| 4ttb | FMN | Iodotyrosine deiodinase 1 | / | 0.815 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.788 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.771 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.771 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.761 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.751 | |
| 3to0 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.746 | |
| 3ge6 | FMN | Nitroreductase | / | 0.744 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.741 | |
| 3e39 | FMN | Nitroreductase | / | 0.737 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.728 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.728 | |
| 4hnb | FMN | LOV protein | / | 0.728 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.723 | |
| 3bem | FMN | Putative NAD(P)H nitroreductase MhqN | 1 | 0.720 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.717 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.713 | |
| 2bkj | FMN | NADPH-flavin oxidoreductase | / | 0.712 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.709 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.709 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.709 | |
| 5ahs | FAD | Acyl-CoA dehydrogenase | / | 0.706 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.705 | |
| 3ukk | FDA | UDP-galactopyranose mutase | / | 0.703 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.701 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.701 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.699 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.698 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.697 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.697 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.697 | |
| 4hj6 | FMN | LOV protein | / | 0.696 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.695 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.695 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.695 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.694 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.688 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.687 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.685 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.685 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.685 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.684 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.684 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.683 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.683 | |
| 4hj4 | FMN | LOV protein | / | 0.683 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.682 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.682 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.682 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.681 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.681 | |
| 3ukl | FAD | UDP-galactopyranose mutase | / | 0.681 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.680 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.680 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.679 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.679 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.678 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.678 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.678 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.677 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.677 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.676 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.676 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.675 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.675 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.675 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.674 | |
| 1vrq | FMN | Subunit alpha of sarocosine oxidase | / | 0.674 | |
| 1vrq | FMN | Subunit beta of sarcosine oxidase | / | 0.674 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.674 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.674 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.673 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.673 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.673 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.673 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.672 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.672 | |
| 5efw | FMN | NPH1-1 | / | 0.672 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.671 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.671 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.670 | |
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 0.670 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 3n39 | FMN | Protein NrdI | / | 0.670 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 1kqc | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.669 | |
| 1um0 | FMN | Chorismate synthase | / | 0.669 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.668 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.668 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.668 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.668 | |
| 1djq | FMN | Trimethylamine dehydrogenase | 1.5.8.2 | 0.667 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.667 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.667 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.667 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.666 | |
| 3ewk | FAD | Sensory box histidine kinase/response regulator | / | 0.665 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.664 | |
| 2gj3 | FAD | Nitrogen fixation regulatory protein | 2.7.13.3 | 0.664 | |
| 3m12 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.664 | |
| 3qfr | FMN | NADPH--cytochrome P450 reductase | / | 0.664 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.663 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.662 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.662 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.662 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.662 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.662 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.661 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.660 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.660 | |
| 3n3a | FMN | Protein NrdI | / | 0.660 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.660 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.660 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.660 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.659 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.659 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.659 | |
| 4yxd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.659 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.659 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.658 | |
| 1p0n | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.658 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.658 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.657 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.657 | |
| 1x31 | FMN | Subunit alpha of sarocosine oxidase | / | 0.657 | |
| 1x31 | FMN | Subunit beta of sarcosine oxidase | / | 0.657 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.657 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.657 | |
| 1zwl | FMN | NAD(P)H dehydrogenase (quinone) | 1.6.5.2 | 0.656 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.656 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.656 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.654 | |
| 3f6s | FMN | Flavodoxin | / | 0.654 | |
| 4k5r | FAD | Oxygenase | / | 0.654 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.653 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.653 | |
| 1v93 | FAD | Methylenetetrahydrofolate reductase | / | 0.653 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.653 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.653 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.653 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.653 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.653 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.652 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.652 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.652 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.652 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.652 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.652 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.651 | |
| 1qr2 | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.651 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.651 | |
| 4bmo | FMN | Protein NrdI | / | 0.650 | |
| 5djt | FMN | NPH1-2 | / | 0.650 |