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 |
|---|---|---|---|
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 1.278 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.159 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.139 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.110 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.083 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.081 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.059 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.997 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.994 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.993 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.986 | |
| 4hia | FMN | LOV protein | / | 0.981 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.977 | |
| 5efw | FMN | NPH1-1 | / | 0.973 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.967 | |
| 4hj6 | FMN | LOV protein | / | 0.966 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.964 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.951 | |
| 4hj3 | FMN | LOV protein | / | 0.943 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.929 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.928 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.928 | |
| 3sw1 | FMN | Sensory box protein | / | 0.925 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.915 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.908 | |
| 4wf0 | FMN | NPH1-1 | / | 0.903 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.901 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.892 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.867 | |
| 5j3w | FMN | Sensory box protein | / | 0.860 | |
| 4hnb | FMN | LOV protein | / | 0.846 | |
| 5djt | FMN | NPH1-2 | / | 0.837 | |
| 4hj4 | FMN | LOV protein | / | 0.827 | |
| 5dju | FMN | NPH1-2 | / | 0.822 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.804 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.803 | |
| 2v0u | FMN | NPH1-1 | / | 0.790 | |
| 5j4e | FMN | Sensory box protein | / | 0.765 | |
| 1g28 | FMN | PHY3 | / | 0.758 | |
| 2v1a | FMN | NPH1-1 | / | 0.751 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.735 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.732 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.715 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.708 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.705 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.702 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.700 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.700 | |
| 1x31 | FMN | Subunit alpha of sarocosine oxidase | / | 0.699 | |
| 1x31 | FMN | Subunit beta of sarcosine oxidase | / | 0.699 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.699 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.699 | |
| 3gg0 | FMN | Uncharacterized protein | / | 0.697 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.695 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.694 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.693 | |
| 1ffu | FAD | Carbon monoxide dehydrogenase medium chain | / | 0.689 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.689 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.689 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.687 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.685 | |
| 3gfx | FMN | Uncharacterized protein | / | 0.685 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.682 | |
| 1usc | FMN | Monooxygenase | / | 0.681 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.681 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.681 | |
| 5cho | FAD | Flavin reductase | / | 0.681 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.678 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.678 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.677 | |
| 2gj3 | FAD | Nitrogen fixation regulatory protein | 2.7.13.3 | 0.677 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.677 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.676 | |
| 2ard | FDA | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.675 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.674 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.673 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.673 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.673 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.672 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.669 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.669 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.668 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.667 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.667 | |
| 3gfy | FMN | Uncharacterized protein | / | 0.665 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.665 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.665 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.664 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.664 | |
| 4k5r | FAD | Oxygenase | / | 0.664 | |
| 3a3b | RBF | Lumazine protein | / | 0.663 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.663 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.662 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.661 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.660 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.659 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.659 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.659 | |
| 1u3d | FAD | Cryptochrome-1 | / | 0.658 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.657 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.657 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.656 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.654 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.654 | |
| 1yrx | FMN | AppA protein | / | 0.654 | |
| 1zy8 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.654 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.654 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.654 | |
| 4j34 | FAD | Kynurenine 3-monooxygenase | / | 0.654 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.653 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.653 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.653 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.653 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.653 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.653 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.653 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.652 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.652 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.651 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.651 | |
| 4h4o | 506 | Gag-Pol polyprotein | 2.7.7.49 | 0.651 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.651 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.651 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.650 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.650 | |
| 1u3c | FAD | Cryptochrome-1 | / | 0.650 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.650 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.650 |