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 |
|---|---|---|---|
| 3is2 | FAD | Vivid PAS protein VVD |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3is2 | FAD | Vivid PAS protein VVD | / | 1.646 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.431 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.423 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.399 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.366 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.365 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.027 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 1.004 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.000 | |
| 5djt | FMN | NPH1-2 | / | 0.994 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.988 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.988 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.955 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.940 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.928 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.927 | |
| 4hj3 | FMN | LOV protein | / | 0.921 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.901 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.896 | |
| 2v1a | FMN | NPH1-1 | / | 0.894 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.883 | |
| 2v0u | FMN | NPH1-1 | / | 0.873 | |
| 5efw | FMN | NPH1-1 | / | 0.853 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.845 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.836 | |
| 5dju | FMN | NPH1-2 | / | 0.831 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.830 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.821 | |
| 4hnb | FMN | LOV protein | / | 0.808 | |
| 4hj6 | FMN | LOV protein | / | 0.805 | |
| 4hj4 | FMN | LOV protein | / | 0.797 | |
| 4wf0 | FMN | NPH1-1 | / | 0.787 | |
| 3sw1 | FMN | Sensory box protein | / | 0.784 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.781 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.772 | |
| 5j3w | FMN | Sensory box protein | / | 0.771 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.725 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.716 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.715 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.698 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.691 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.691 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.689 | |
| 4hia | FMN | LOV protein | / | 0.687 | |
| 5j4e | FMN | Sensory box protein | / | 0.679 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.674 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.673 | |
| 5cho | FAD | Flavin reductase | / | 0.672 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.672 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.669 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.667 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.666 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.665 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.664 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.663 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.660 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.660 | |
| 4hmx | FMN | Pyridoxamine 5'-phosphate oxidase | / | 0.660 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.660 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.659 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.659 | |
| 4irn | FAD | AnaB | / | 0.658 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.657 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.657 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.657 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.656 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.655 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.655 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.655 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.654 | |
| 1wv4 | FMN | Pyridoxine/pyridoxamine 5'-phosphate oxidase | / | 0.654 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.654 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.654 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.653 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.652 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.651 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.651 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.650 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 |