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 |
|---|---|---|---|
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.372 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.125 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 1.091 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.885 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.870 | |
| 1ooq | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.849 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.844 | |
| 4ttb | FMN | Iodotyrosine deiodinase 1 | / | 0.842 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.830 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.818 | |
| 3e39 | FMN | Nitroreductase | / | 0.816 | |
| 3to0 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.816 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.814 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.810 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.809 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.809 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.805 | |
| 3bem | FMN | Putative NAD(P)H nitroreductase MhqN | 1 | 0.803 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.801 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.785 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.784 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.784 | |
| 1kqb | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.778 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.777 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.776 | |
| 1kqc | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.776 | |
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 0.775 | |
| 4xoo | FMN | Coenzyme F420:L-glutamate ligase | / | 0.775 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.774 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.767 | |
| 2bkj | FMN | NADPH-flavin oxidoreductase | / | 0.765 | |
| 1ylr | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.764 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.763 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.761 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.753 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.750 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.743 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.742 | |
| 3koq | FMN | Putative nitroreductase | / | 0.737 | |
| 3pxv | FMN | Nitroreductase | / | 0.727 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.717 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.710 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.708 | |
| 3eof | FMN | Putative oxidase | / | 0.707 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.706 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.706 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.705 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.704 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.704 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.702 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.702 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.700 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.700 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.700 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.699 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.699 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.699 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.699 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.699 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.699 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.698 | |
| 5efw | FMN | NPH1-1 | / | 0.698 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.697 | |
| 4hj4 | FMN | LOV protein | / | 0.695 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.693 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.693 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.693 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.692 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.692 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.691 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.691 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.690 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.690 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.690 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.688 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.688 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.687 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.687 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.685 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.685 | |
| 3x21 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.685 | |
| 1um0 | FMN | Chorismate synthase | / | 0.684 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.684 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.680 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.678 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.678 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.678 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.676 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.676 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.676 | |
| 1eje | FMN | Protein MTH_152 | / | 0.675 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.675 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.675 | |
| 4hia | FMN | LOV protein | / | 0.675 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.675 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.674 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.674 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.674 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.674 | |
| 3g5m | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.674 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.674 | |
| 3rha | FDA | Putrescine oxidase | / | 0.674 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.672 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.672 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.672 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.671 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.671 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.670 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.669 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.669 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.669 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.668 | |
| 3uwq | U5P | Orotidine 5'-phosphate decarboxylase | / | 0.668 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.667 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.667 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.667 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.666 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.666 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.666 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.664 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.664 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.663 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.663 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.663 | |
| 4bmo | FMN | Protein NrdI | / | 0.663 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.662 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.662 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.662 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.662 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.661 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.661 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.661 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.660 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.660 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.660 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.659 | |
| 4fdp | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.659 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.658 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.656 | |
| 4emj | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.656 | |
| 4h4s | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.656 | |
| 2e77 | FMN | Lactate oxidase | / | 0.655 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.655 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.655 | |
| 4zvl | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.655 | |
| 2bn4 | FMN | NADPH--cytochrome P450 reductase | / | 0.654 | |
| 3f6s | FMN | Flavodoxin | / | 0.654 | |
| 3n3b | FMN | Protein NrdI | / | 0.654 | |
| 4f4q | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.653 | |
| 4h4w | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.653 | |
| 4jic | FMN | GTN Reductase | / | 0.653 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.653 | |
| 3r6c | 17N | Anthranilate phosphoribosyltransferase | / | 0.652 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.652 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.652 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.651 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.651 | |
| 4fdn | FAD | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.651 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.651 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.650 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.650 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.650 |