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 |
|---|---|---|---|
| 4hia | FMN | LOV protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4hia | FMN | LOV protein | / | 1.354 | |
| 4hj6 | FMN | LOV protein | / | 1.263 | |
| 4hj3 | FMN | LOV protein | / | 1.135 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 1.058 | |
| 4hj4 | FMN | LOV protein | / | 1.028 | |
| 4hnb | FMN | LOV protein | / | 1.014 | |
| 1n9n | FMN | Putative blue light receptor | / | 1.013 | |
| 5j3w | FMN | Sensory box protein | / | 0.993 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.989 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.987 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.982 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.981 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.967 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.958 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.953 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.951 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.949 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.944 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.924 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.916 | |
| 5efw | FMN | NPH1-1 | / | 0.912 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.911 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.899 | |
| 5djt | FMN | NPH1-2 | / | 0.888 | |
| 5j4e | FMN | Sensory box protein | / | 0.887 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.885 | |
| 2v1a | FMN | NPH1-1 | / | 0.883 | |
| 2v0u | FMN | NPH1-1 | / | 0.872 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.852 | |
| 1g28 | FMN | PHY3 | / | 0.842 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.834 | |
| 5dju | FMN | NPH1-2 | / | 0.810 | |
| 4wf0 | FMN | NPH1-1 | / | 0.781 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.758 | |
| 3sw1 | FMN | Sensory box protein | / | 0.745 | |
| 2a1u | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.734 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.734 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.730 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.729 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.724 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.719 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.719 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.714 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.713 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.708 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.707 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.706 | |
| 4h6r | FDA | Proline dehydrogenase | / | 0.705 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.704 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.704 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.701 | |
| 3gfx | FMN | Uncharacterized protein | / | 0.697 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.697 | |
| 1ep3 | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | / | 0.696 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.696 | |
| 1usc | FMN | Monooxygenase | / | 0.696 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.696 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.696 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.695 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.694 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.693 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.693 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.692 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.692 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.692 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.691 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.690 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.690 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.689 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.688 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.687 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.687 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.687 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.684 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.684 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.683 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 3m12 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.683 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.683 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.682 | |
| 4irn | FAD | AnaB | / | 0.682 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.682 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.681 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.680 | |
| 3e9y | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.679 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.679 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.678 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.678 | |
| 3a3b | RBF | Lumazine protein | / | 0.678 | |
| 4hh0 | FMN | AppA protein | / | 0.678 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.678 | |
| 1jue | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.677 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.677 | |
| 4ocg | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.677 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.677 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.676 | |
| 3gfy | FMN | Uncharacterized protein | / | 0.676 | |
| 3mbg | FAD | FAD-linked sulfhydryl oxidase ALR | 1.8.3.2 | 0.676 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.676 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.675 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.675 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.675 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.674 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.674 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.673 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.672 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.671 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 3ea4 | FAB | Acetolactate synthase, chloroplastic | 2.2.1.6 | 0.671 | |
| 4h4u | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.671 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.670 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1gox | FMN | Peroxisomal (S)-2-hydroxy-acid oxidase | 1.1.3.15 | 0.669 | |
| 3bnk | FMN | Flavoredoxin | / | 0.669 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.669 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.668 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.668 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.668 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.668 | |
| 1gxf | FAD | Trypanothione reductase | 1.8.1.12 | 0.667 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.667 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.667 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.667 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.666 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.666 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.666 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.665 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.665 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.665 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 1r2j | FAD | FkbI | / | 0.663 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.663 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.662 | |
| 1s4m | LUM | Riboflavin biosynthesis protein | / | 0.661 | |
| 2j4d | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.661 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.661 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.660 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.660 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.660 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.660 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.660 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.660 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.659 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.659 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.659 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.659 | |
| 5dkk | FMN | Predicted protein | / | 0.659 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.658 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.658 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.658 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.658 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.658 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.657 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.657 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.657 | |
| 2mwg | FMN | Blue-light photoreceptor | / | 0.657 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.657 | |
| 1yrx | FMN | AppA protein | / | 0.656 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.656 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.656 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.655 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.655 | |
| 3f6s | FMN | Flavodoxin | / | 0.654 | |
| 3giy | FMN | (S)-mandelate dehydrogenase | 1.1.99.31 | 0.654 | |
| 3qzy | FAD | FAD-linked sulfhydryl oxidase | / | 0.654 | |
| 2cfy | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.653 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.653 | |
| 2yvf | FAD | Ferredoxin reductase | / | 0.653 | |
| 1qlt | FAD | Vanillyl-alcohol oxidase | 1.1.3.38 | 0.652 | |
| 4zvn | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.652 | |
| 1d7l | RFL | p-hydroxybenzoate hydroxylase | / | 0.651 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.651 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.651 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.651 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.650 | |
| 4l06 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.650 |