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 |
|---|---|---|---|
| 2pdt | FAD | Vivid PAS protein VVD |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.332 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.173 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.166 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.148 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.144 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.060 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.048 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.046 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.028 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 1.027 | |
| 5djt | FMN | NPH1-2 | / | 1.003 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.002 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.997 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.985 | |
| 2v1a | FMN | NPH1-1 | / | 0.985 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.982 | |
| 2v0u | FMN | NPH1-1 | / | 0.976 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.957 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.954 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.953 | |
| 4hj6 | FMN | LOV protein | / | 0.948 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.936 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.930 | |
| 4hia | FMN | LOV protein | / | 0.924 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.921 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.920 | |
| 5dju | FMN | NPH1-2 | / | 0.907 | |
| 5efw | FMN | NPH1-1 | / | 0.901 | |
| 5j3w | FMN | Sensory box protein | / | 0.893 | |
| 4hj3 | FMN | LOV protein | / | 0.887 | |
| 4hnb | FMN | LOV protein | / | 0.885 | |
| 1g28 | FMN | PHY3 | / | 0.860 | |
| 5j4e | FMN | Sensory box protein | / | 0.856 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.841 | |
| 4hj4 | FMN | LOV protein | / | 0.809 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.797 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.793 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.785 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.775 | |
| 3sw1 | FMN | Sensory box protein | / | 0.742 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.723 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.721 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.716 | |
| 4wf0 | FMN | NPH1-1 | / | 0.713 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.709 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.699 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.699 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.695 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.694 | |
| 5dkk | FMN | Predicted protein | / | 0.694 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.692 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.689 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.689 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.689 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.688 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.688 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.688 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.686 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.685 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.684 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.681 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.680 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.680 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.680 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.678 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.677 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.676 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.676 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.675 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.675 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.674 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.674 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.672 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.672 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.672 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.672 | |
| 4a65 | FAD | Thioredoxin reductase | / | 0.672 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.671 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.671 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.670 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.670 | |
| 5cho | FAD | Flavin reductase | / | 0.670 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.669 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.668 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.668 | |
| 3a3b | RBF | Lumazine protein | / | 0.668 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.667 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.667 | |
| 1yrx | FMN | AppA protein | / | 0.666 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.665 | |
| 2ou5 | FMN | Pyridoxamine 5'-phosphate oxidase-related FMN-binding protein | / | 0.665 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.665 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.665 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.665 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.664 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.664 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.664 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.664 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.663 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.663 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.663 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.663 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.663 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.661 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.661 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.661 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.660 | |
| 4bl5 | GFB | GDP-L-fucose synthase | 1.1.1.271 | 0.660 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.660 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 4cbq | FAD | Thioredoxin reductase | / | 0.659 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.658 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.658 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.657 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.657 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.656 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.656 | |
| 2j09 | FMN | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.656 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.656 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.656 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.656 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.655 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.655 | |
| 3rha | FDA | Putrescine oxidase | / | 0.655 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.655 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.654 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.654 | |
| 4ccr | FAD | Thioredoxin reductase | / | 0.653 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.652 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.652 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.652 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.652 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.652 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.651 | |
| 3bm1 | FMN | Putative NAD(P)H nitroreductase YdjA | / | 0.651 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.651 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.651 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.650 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.650 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.650 |