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 |
|---|---|---|---|
| 4kuk | RBF | Putative blue-light photoreceptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4kuk | RBF | Putative blue-light photoreceptor | / | 1.202 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 1.120 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.025 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.008 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.992 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.985 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.974 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.961 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.954 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.946 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.944 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.928 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.926 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.926 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.905 | |
| 4wf0 | FMN | NPH1-1 | / | 0.899 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.898 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.886 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.881 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.862 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.860 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.845 | |
| 4hj3 | FMN | LOV protein | / | 0.839 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.828 | |
| 5djt | FMN | NPH1-2 | / | 0.795 | |
| 5j3w | FMN | Sensory box protein | / | 0.781 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.780 | |
| 5efw | FMN | NPH1-1 | / | 0.779 | |
| 5j4e | FMN | Sensory box protein | / | 0.758 | |
| 3sw1 | FMN | Sensory box protein | / | 0.757 | |
| 4hj4 | FMN | LOV protein | / | 0.749 | |
| 5dju | FMN | NPH1-2 | / | 0.746 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.732 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.732 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.731 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.728 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.716 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.715 | |
| 5dkk | FMN | Predicted protein | / | 0.713 | |
| 1yrx | FMN | AppA protein | / | 0.710 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.710 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.707 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.706 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.705 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.704 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.701 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.701 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.701 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.700 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.699 | |
| 4hh0 | FMN | AppA protein | / | 0.698 | |
| 3a3b | RBF | Lumazine protein | / | 0.696 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.696 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.695 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.692 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.691 | |
| 2v0u | FMN | NPH1-1 | / | 0.691 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.689 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.689 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.688 | |
| 4hia | FMN | LOV protein | / | 0.688 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.687 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.686 | |
| 2vxa | RBF | Dodecin | / | 0.685 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.685 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.684 | |
| 4jic | FMN | GTN Reductase | / | 0.684 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.684 | |
| 1p0n | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.682 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.681 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.681 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.680 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.680 | |
| 3a3g | DLZ | Lumazine protein | / | 0.678 | |
| 3bnk | FMN | Flavoredoxin | / | 0.677 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.677 | |
| 1lm1 | FMN | Ferredoxin-dependent glutamate synthase 2 | 1.4.7.1 | 0.676 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.676 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.676 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.675 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.675 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.673 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.672 | |
| 2hsa | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.672 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.672 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.671 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.671 | |
| 4irn | FAD | AnaB | / | 0.671 | |
| 1gaq | FAD | Ferredoxin | / | 0.670 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.670 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.670 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.670 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.669 | |
| 4hj6 | FMN | LOV protein | / | 0.669 | |
| 1eje | FMN | Protein MTH_152 | / | 0.668 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.668 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.668 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.668 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.668 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.668 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.667 | |
| 1buc | FAD | Acyl-CoA dehydrogenase, short-chain specific | 1.3.8.1 | 0.666 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.666 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.666 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.666 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.665 | |
| 4hnb | FMN | LOV protein | / | 0.665 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.664 | |
| 4h2p | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.664 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.663 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.663 | |
| 2o12 | FMN | Chorismate synthase | / | 0.663 | |
| 3qzy | FAD | FAD-linked sulfhydryl oxidase | / | 0.663 | |
| 5cho | FAD | Flavin reductase | / | 0.663 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.662 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.662 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.662 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.662 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.662 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.662 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.661 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.661 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.661 | |
| 1rq1 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.660 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.660 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.660 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.659 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.659 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.659 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.659 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.658 | |
| 3m31 | FAD | Endoplasmic oxidoreductin-1 | 1.8.4 | 0.658 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.657 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.657 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.657 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.657 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.656 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.656 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.655 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.655 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.654 | |
| 3p4t | FAO | Putative acyl-CoA dehydrogenase | / | 0.654 | |
| 4e2d | FMN | Dehydrogenase | / | 0.654 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.654 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.653 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.653 | |
| 4qof | FMN | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.653 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.652 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.652 | |
| 1qlt | FAD | Vanillyl-alcohol oxidase | 1.1.3.38 | 0.651 | |
| 4jy2 | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.651 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.650 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.650 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.650 | |
| 4qoe | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.650 |