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 |
|---|---|---|---|
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.321 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.172 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.130 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.121 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.109 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 1.059 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 1.059 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.038 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.029 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 1.008 | |
| 2v1a | FMN | NPH1-1 | / | 1.000 | |
| 2v0u | FMN | NPH1-1 | / | 0.995 | |
| 5dju | FMN | NPH1-2 | / | 0.994 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.993 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.991 | |
| 4hj6 | FMN | LOV protein | / | 0.991 | |
| 5efw | FMN | NPH1-1 | / | 0.990 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.985 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.984 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.982 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.965 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.961 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.961 | |
| 4wf0 | FMN | NPH1-1 | / | 0.954 | |
| 5djt | FMN | NPH1-2 | / | 0.932 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.923 | |
| 5j4e | FMN | Sensory box protein | / | 0.916 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.903 | |
| 4hia | FMN | LOV protein | / | 0.899 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.890 | |
| 4hj3 | FMN | LOV protein | / | 0.890 | |
| 1g28 | FMN | PHY3 | / | 0.881 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.836 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.823 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.821 | |
| 5j3w | FMN | Sensory box protein | / | 0.821 | |
| 3sw1 | FMN | Sensory box protein | / | 0.795 | |
| 4hj4 | FMN | LOV protein | / | 0.795 | |
| 4hnb | FMN | LOV protein | / | 0.783 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.767 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.743 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.728 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.725 | |
| 3aeb | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.716 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.715 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.714 | |
| 3gfx | FMN | Uncharacterized protein | / | 0.711 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.709 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.708 | |
| 2bkj | FMN | NADPH-flavin oxidoreductase | / | 0.708 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.708 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.707 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.707 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.705 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.704 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.698 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.698 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.696 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.694 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.693 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.692 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.692 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.691 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.690 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 1yrx | FMN | AppA protein | / | 0.689 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.689 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.685 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.685 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.684 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.684 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.683 | |
| 2v18 | FMN | Dodecin | / | 0.682 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.682 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.682 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.681 | |
| 3gfy | FMN | Uncharacterized protein | / | 0.679 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.679 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.679 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.679 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.678 | |
| 3gfz | FMN | Uncharacterized protein | / | 0.677 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.677 | |
| 1usc | FMN | Monooxygenase | / | 0.676 | |
| 4hh0 | FMN | AppA protein | / | 0.676 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.676 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.676 | |
| 3fst | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.674 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.674 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.673 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.673 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.672 | |
| 5dkk | FMN | Predicted protein | / | 0.672 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.671 | |
| 2vxa | RBF | Dodecin | / | 0.671 | |
| 2yyi | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.671 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.671 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.671 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 4jn9 | FAD | DepH | / | 0.669 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.668 | |
| 1nb9 | RBF | Riboflavin kinase | 2.7.1.26 | 0.667 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.667 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.667 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.667 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.667 | |
| 2bac | FAD | Putative aminooxidase | / | 0.666 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.666 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.666 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.665 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.665 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.664 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.664 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.664 | |
| 3qzy | FAD | FAD-linked sulfhydryl oxidase | / | 0.664 | |
| 4iil | RBF | Membrane lipoprotein TpN38(b) | / | 0.664 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.664 | |
| 1v93 | FAD | Methylenetetrahydrofolate reductase | / | 0.663 | |
| 3fsu | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.663 | |
| 4nte | FAD | DepH | / | 0.663 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.663 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.662 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.662 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.662 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.662 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.661 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.661 | |
| 1p4m | FMN | Riboflavin kinase | 2.7.1.26 | 0.661 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.661 | |
| 2qa1 | FAD | PgaE | / | 0.661 | |
| 3u33 | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.661 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.661 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.660 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.659 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.659 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.658 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.658 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.658 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.657 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.657 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.656 | |
| 3bnk | FMN | Flavoredoxin | / | 0.656 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.656 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.656 | |
| 4e2b | FMN | Dehydrogenase | / | 0.656 | |
| 5ahk | FAD | Acetolactate synthase II, large subunit | / | 0.656 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.655 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.655 | |
| 2yyl | FAD | 4-hydroxyphenylacetate 3-monooxygenase oxygenase component | 1.14.14.9 | 0.655 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.654 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.654 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.654 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.654 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.654 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.653 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.653 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.653 | |
| 4irn | FAD | AnaB | / | 0.653 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.652 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 1owo | FAD | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.652 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.652 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.651 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.651 |