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 |
|---|---|---|---|
| 2pr5 | FMN | Blue-light photoreceptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.376 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.193 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.159 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 1.129 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.117 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.115 | |
| 5djt | FMN | NPH1-2 | / | 1.112 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 1.083 | |
| 2v0u | FMN | NPH1-1 | / | 1.040 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.038 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 1.025 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.020 | |
| 1n9n | FMN | Putative blue light receptor | / | 1.009 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 1.007 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.990 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.982 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.971 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.953 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.925 | |
| 4hia | FMN | LOV protein | / | 0.916 | |
| 4hj3 | FMN | LOV protein | / | 0.916 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.913 | |
| 4hj6 | FMN | LOV protein | / | 0.910 | |
| 2v1a | FMN | NPH1-1 | / | 0.908 | |
| 5j3w | FMN | Sensory box protein | / | 0.904 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.896 | |
| 5efw | FMN | NPH1-1 | / | 0.885 | |
| 5dju | FMN | NPH1-2 | / | 0.857 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.842 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.832 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.830 | |
| 3sw1 | FMN | Sensory box protein | / | 0.812 | |
| 4wf0 | FMN | NPH1-1 | / | 0.811 | |
| 4hnb | FMN | LOV protein | / | 0.806 | |
| 1g28 | FMN | PHY3 | / | 0.797 | |
| 2a1u | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.746 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.738 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.735 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.729 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.728 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.727 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.726 | |
| 4irn | FAD | AnaB | / | 0.724 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.722 | |
| 1yrx | FMN | AppA protein | / | 0.721 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.721 | |
| 1usc | FMN | Monooxygenase | / | 0.718 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.718 | |
| 5j4e | FMN | Sensory box protein | / | 0.716 | |
| 4hj4 | FMN | LOV protein | / | 0.715 | |
| 3da1 | FAD | Glycerol-3-phosphate dehydrogenase | / | 0.713 | |
| 4hh0 | FMN | AppA protein | / | 0.713 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.712 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.711 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.710 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.710 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.709 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.708 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.707 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.704 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.703 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.701 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.700 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.700 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.700 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.698 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.698 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.698 | |
| 1t6y | FMN | Riboflavin biosynthesis protein | / | 0.697 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.697 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.697 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.696 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.695 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.694 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.693 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.693 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.692 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.692 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.691 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.690 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.690 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.688 | |
| 5cho | FAD | Flavin reductase | / | 0.687 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.687 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.686 | |
| 3gfx | FMN | Uncharacterized protein | / | 0.686 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.685 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.685 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.685 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.683 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.682 | |
| 3mdd | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.682 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.681 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.681 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.681 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.680 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.679 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.679 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.679 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.679 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.678 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.678 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.677 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.677 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.677 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.676 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.676 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.676 | |
| 5dkk | FMN | Predicted protein | / | 0.676 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.675 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.674 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.673 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.673 | |
| 2wow | FAD | Trypanothione reductase | / | 0.673 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.673 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.673 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.673 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.672 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.671 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.671 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.670 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.670 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.670 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.669 | |
| 2bac | FAD | Putative aminooxidase | / | 0.669 | |
| 3lzw | NAP | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.669 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.669 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.668 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.667 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.667 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.666 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.666 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.666 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.666 | |
| 1kqb | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.665 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.665 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.665 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.665 | |
| 4cw5 | FMN | DfnA | / | 0.665 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.665 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.665 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.664 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.664 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.664 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.664 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.664 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.664 | |
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 0.663 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.663 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.662 | |
| 2gmj | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.662 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.662 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.662 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.662 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.661 | |
| 2cdu | FAD | NADH oxidase | / | 0.661 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.661 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.661 | |
| 3itj | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.661 | |
| 4e2d | FMN | Dehydrogenase | / | 0.661 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.660 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.660 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.660 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.660 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.660 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.659 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.659 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.659 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.659 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.659 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.658 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.658 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.658 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.658 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.658 | |
| 1qgz | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.657 | |
| 1um0 | FMN | Chorismate synthase | / | 0.657 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.657 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.657 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.657 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 0.656 | |
| 1yy5 | FAD | Polyamine oxidase FMS1 | / | 0.656 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.656 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.656 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.656 | |
| 3up5 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.656 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.655 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.655 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.655 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.655 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.655 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.654 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.654 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.654 | |
| 2ed4 | FAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.653 | |
| 2ix5 | FAD | Acyl-coenzyme A oxidase 4, peroxisomal | 1.3.3.6 | 0.653 | |
| 3fbs | FAD | Oxidoreductase | / | 0.653 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.653 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.653 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.652 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.652 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.652 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.652 | |
| 1rz1 | FAD | Phenol 2-hydroxylase component B | / | 0.651 | |
| 2e48 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.651 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.651 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.651 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.651 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.650 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.650 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.650 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.650 |