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 |
|---|---|---|---|
| 4eet | FMN | Phototropin-2 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.380 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.240 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.198 | |
| 5djt | FMN | NPH1-2 | / | 1.156 | |
| 5efw | FMN | NPH1-1 | / | 1.122 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.117 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 1.110 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 1.108 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.106 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.060 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.048 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.046 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.044 | |
| 5dju | FMN | NPH1-2 | / | 1.042 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.038 | |
| 4hj6 | FMN | LOV protein | / | 1.032 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.031 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.030 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.029 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 1.000 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.979 | |
| 4hj3 | FMN | LOV protein | / | 0.971 | |
| 4hia | FMN | LOV protein | / | 0.967 | |
| 4wf0 | FMN | NPH1-1 | / | 0.958 | |
| 3sw1 | FMN | Sensory box protein | / | 0.938 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.938 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.935 | |
| 2v0u | FMN | NPH1-1 | / | 0.929 | |
| 2v1a | FMN | NPH1-1 | / | 0.912 | |
| 1g28 | FMN | PHY3 | / | 0.904 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.898 | |
| 5j3w | FMN | Sensory box protein | / | 0.888 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.874 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.856 | |
| 4hj4 | FMN | LOV protein | / | 0.841 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.828 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.812 | |
| 4hnb | FMN | LOV protein | / | 0.792 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.762 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.761 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.737 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.730 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.725 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.723 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.714 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.707 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.702 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.699 | |
| 2ou5 | FMN | Pyridoxamine 5'-phosphate oxidase-related FMN-binding protein | / | 0.698 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.698 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.697 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.695 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.695 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.694 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.694 | |
| 5dkk | FMN | Predicted protein | / | 0.692 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.691 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.691 | |
| 5by6 | UMP | Thymidylate synthase | / | 0.690 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.689 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.688 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.687 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.686 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.686 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.686 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.685 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.684 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.683 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.682 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.682 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.682 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.680 | |
| 3ojx | FAD | NADPH--cytochrome P450 reductase | / | 0.680 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.680 | |
| 5cho | FAD | Flavin reductase | / | 0.680 | |
| 5ahs | FAD | Acyl-CoA dehydrogenase | / | 0.679 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.678 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.678 | |
| 4jnq | FDA | Thioredoxin reductase | / | 0.677 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.677 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.676 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.676 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.675 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.675 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.675 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.675 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.673 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.673 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.673 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.672 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.672 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.671 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.671 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.669 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.668 | |
| 4k5r | FAD | Oxygenase | / | 0.668 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.668 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.667 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.667 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.667 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.667 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.666 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.666 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.665 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.665 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.664 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.664 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.664 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.664 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.664 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.664 | |
| 4yaf | FAD | NADPH--cytochrome P450 reductase | / | 0.664 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.662 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.662 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.662 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.661 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.661 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.661 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.660 | |
| 2j09 | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.660 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.660 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.660 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.659 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.659 | |
| 3qzy | FAD | FAD-linked sulfhydryl oxidase | / | 0.659 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.659 | |
| 1qgz | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.658 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.658 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.658 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.658 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.657 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.657 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.657 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.657 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.656 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.656 | |
| 4icy | FAD | PgaE | / | 0.656 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.655 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.655 | |
| 4dq1 | UMP | Thymidylate synthase | / | 0.655 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.655 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.655 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.654 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.653 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.653 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.653 | |
| 1gr1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.652 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.651 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.651 | |
| 4cdg | ADP | Bloom syndrome protein | 3.6.4.12 | 0.651 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.651 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.650 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.650 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.650 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.650 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.650 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.650 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.650 |