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 |
|---|---|---|---|
| 2dvl | FAD | Acyl-CoA dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 1.195 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.950 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.945 | |
| 2d29 | FAD | Acyl-CoA dehydrogenase | / | 0.904 | |
| 1egd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.903 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.901 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.890 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.886 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.883 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.881 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.879 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.875 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.851 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.848 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.841 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.839 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.837 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.835 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.830 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.829 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.825 | |
| 1r2j | FAD | FkbI | / | 0.819 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.816 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.813 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.798 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.797 | |
| 2eba | FAD | Putative glutaryl-CoA dehydrogenase | / | 0.787 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.780 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.763 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.753 | |
| 3owa | FAD | Acyl-CoA dehydrogenase | / | 0.753 | |
| 4irn | FAD | AnaB | / | 0.738 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.731 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.721 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.716 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.715 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.715 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.704 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.701 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.700 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.697 | |
| 5j4e | FMN | Sensory box protein | / | 0.697 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.695 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.695 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.693 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.693 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.693 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.689 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.688 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.688 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.687 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.686 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.685 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.680 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.680 | |
| 1gaq | FAD | Ferredoxin | / | 0.679 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.679 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.678 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.678 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.678 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.678 | |
| 2h8x | FMN | XenA | / | 0.677 | |
| 1ep1 | FMN | Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit | 1.3.1.14 | 0.676 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.676 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.676 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.675 | |
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 0.674 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.674 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.674 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.672 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.671 | |
| 3w5u | FAD | Ferredoxin | / | 0.671 | |
| 2e77 | FMN | Lactate oxidase | / | 0.669 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.669 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.668 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.667 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.667 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.667 | |
| 4k5r | FAD | Oxygenase | / | 0.667 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 5a89 | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.667 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.667 | |
| 2cdu | FAD | NADH oxidase | / | 0.666 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.666 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.666 | |
| 2q9u | FMN | A-type flavoprotein | / | 0.665 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.665 | |
| 5efw | FMN | NPH1-1 | / | 0.665 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.663 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3n39 | FMN | Protein NrdI | / | 0.663 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.663 | |
| 1ofv | FMN | Flavodoxin | / | 0.662 | |
| 2fon | FAD | Acyl-coenzyme A oxidase | / | 0.662 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.661 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.660 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.660 | |
| 3ka7 | FAD | Putative oxidoreductase | / | 0.660 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.660 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.660 | |
| 2j07 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.659 | |
| 4h6p | FMN | Chromate reductase | / | 0.659 | |
| 4jy2 | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.659 | |
| 1czn | FMN | Flavodoxin | / | 0.658 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.658 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.658 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.657 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.657 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.656 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.655 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.655 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.654 | |
| 1wsb | FMN | Flavodoxin | / | 0.654 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.654 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.654 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.653 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.653 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.653 | |
| 3qj4 | FAD | Renalase | / | 0.653 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.653 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 1yy5 | FAD | Polyamine oxidase FMS1 | / | 0.652 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.652 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.652 | |
| 3l67 | FMN | Xenobiotic reductase | / | 0.652 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.652 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.651 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.651 | |
| 1q1r | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.650 | |
| 1uum | FMN | Dihydroorotate dehydrogenase (quinone), mitochondrial | 1.3.5.2 | 0.650 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.650 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.650 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.650 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.650 |