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 |
|---|---|---|---|
| 4hj4 | FMN | LOV protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4hj4 | FMN | LOV protein | / | 1.248 | |
| 4hj6 | FMN | LOV protein | / | 1.054 | |
| 4hia | FMN | LOV protein | / | 1.028 | |
| 4hj3 | FMN | LOV protein | / | 1.019 | |
| 4hnb | FMN | LOV protein | / | 1.013 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.862 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.860 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.841 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.837 | |
| 5j3w | FMN | Sensory box protein | / | 0.835 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.827 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.817 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.809 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.797 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.795 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.794 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.793 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.792 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.786 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.786 | |
| 5efw | FMN | NPH1-1 | / | 0.778 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.761 | |
| 4wf0 | FMN | NPH1-1 | / | 0.756 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.755 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.749 | |
| 5dju | FMN | NPH1-2 | / | 0.743 | |
| 5djt | FMN | NPH1-2 | / | 0.730 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.725 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.723 | |
| 2v1a | FMN | NPH1-1 | / | 0.723 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.723 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.721 | |
| 5cho | FAD | Flavin reductase | / | 0.718 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.714 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.709 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.704 | |
| 5j4e | FMN | Sensory box protein | / | 0.699 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.695 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.693 | |
| 2v0u | FMN | NPH1-1 | / | 0.693 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.692 | |
| 3haz | FAD | Bifunctional protein PutA | / | 0.692 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.690 | |
| 1x0p | FAD | Tll0078 protein | / | 0.690 | |
| 1g28 | FMN | PHY3 | / | 0.689 | |
| 3sw1 | FMN | Sensory box protein | / | 0.688 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.688 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.687 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.687 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.687 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.686 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.686 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.685 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.684 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.684 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.684 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.683 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.683 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.683 | |
| 4irn | FAD | AnaB | / | 0.682 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.680 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.680 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.679 | |
| 4nm9 | FAD | Bifunctional protein PutA | / | 0.679 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.678 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.678 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.678 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.677 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.677 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.677 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.676 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.676 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.676 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.676 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.675 | |
| 4nmb | FAD | Bifunctional protein PutA | / | 0.675 | |
| 5dkk | FMN | Predicted protein | / | 0.675 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.674 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.674 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.673 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.673 | |
| 4h4u | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.673 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.672 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.670 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.669 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.669 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.668 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.667 | |
| 2bry | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.667 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.667 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.667 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.667 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.667 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.666 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.666 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.666 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.666 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.666 | |
| 2vxa | RBF | Dodecin | / | 0.664 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.664 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.663 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.663 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.662 | |
| 2gj3 | FAD | Nitrogen fixation regulatory protein | 2.7.13.3 | 0.662 | |
| 1tez | HDF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.661 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.661 | |
| 3u2l | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.661 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.660 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.660 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.659 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1s4m | LUM | Riboflavin biosynthesis protein | / | 0.658 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.658 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.658 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.658 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.658 | |
| 3u5s | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.658 | |
| 4xoo | FMN | Coenzyme F420:L-glutamate ligase | / | 0.658 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.657 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.657 | |
| 3n39 | FMN | Protein NrdI | / | 0.657 | |
| 3n3b | FMN | Protein NrdI | / | 0.657 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.657 | |
| 1gaq | FAD | Ferredoxin | / | 0.656 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.655 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.655 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.655 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.654 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.654 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.654 | |
| 3a20 | FMN | FMN-binding protein | / | 0.654 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.653 | |
| 2yvf | FAD | Ferredoxin reductase | / | 0.653 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.653 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.653 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.653 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.652 | |
| 3a6r | FMN | FMN-binding protein | / | 0.652 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.652 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.651 | |
| 3mbg | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.651 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.651 | |
| 1jub | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.650 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.650 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.650 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.650 |