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 |
|---|---|---|---|
| 4ees | FMN | Phototropin-2 | 2.7.11.1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.393 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.240 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.215 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.199 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 1.193 | |
| 5djt | FMN | NPH1-2 | / | 1.167 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 1.139 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 1.109 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.089 | |
| 5efw | FMN | NPH1-1 | / | 1.080 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.073 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 1.059 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.053 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.028 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.028 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.010 | |
| 2v1a | FMN | NPH1-1 | / | 1.009 | |
| 5dju | FMN | NPH1-2 | / | 1.009 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.002 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.992 | |
| 2v0u | FMN | NPH1-1 | / | 0.989 | |
| 4hia | FMN | LOV protein | / | 0.989 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.988 | |
| 4wf0 | FMN | NPH1-1 | / | 0.984 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.975 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.956 | |
| 3sw1 | FMN | Sensory box protein | / | 0.945 | |
| 4hj3 | FMN | LOV protein | / | 0.927 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.919 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.903 | |
| 1g28 | FMN | PHY3 | / | 0.858 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.857 | |
| 4hnb | FMN | LOV protein | / | 0.846 | |
| 4hj4 | FMN | LOV protein | / | 0.837 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.777 | |
| 5j3w | FMN | Sensory box protein | / | 0.762 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.760 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.733 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.723 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.722 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.721 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.715 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.712 | |
| 3djl | FAD | Putative acyl-CoA dehydrogenase AidB | 1.3.99 | 0.708 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.706 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.706 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.700 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.696 | |
| 5cho | FAD | Flavin reductase | / | 0.696 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.694 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.694 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.691 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.691 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.691 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.691 | |
| 1czn | FMN | Flavodoxin | / | 0.690 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.690 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.689 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 5dkk | FMN | Predicted protein | / | 0.688 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.687 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.686 | |
| 3c3n | FMN | Dihydroorotate dehydrogenase (fumarate) | 1.3.98.1 | 0.686 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.686 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.684 | |
| 4bl5 | GFB | GDP-L-fucose synthase | 1.1.1.271 | 0.683 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.682 | |
| 3nix | FAD | Flavoprotein/dehydrogenase | / | 0.682 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.680 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.679 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.677 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.677 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.677 | |
| 1b2r | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.675 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.675 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.674 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.673 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.673 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.672 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.672 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.671 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.671 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.671 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.671 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.671 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.669 | |
| 4jn9 | FAD | DepH | / | 0.669 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.668 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.668 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.666 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.666 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.666 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.665 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.665 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.665 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.664 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.664 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.663 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.663 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.663 | |
| 5j4e | FMN | Sensory box protein | / | 0.663 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.662 | |
| 3lad | FAD | Dihydrolipoyl dehydrogenase | / | 0.662 | |
| 4cbq | FAD | Thioredoxin reductase | / | 0.662 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.662 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.661 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.661 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.661 | |
| 5fs8 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.661 | |
| 1eje | FMN | Protein MTH_152 | / | 0.660 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.660 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.660 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.660 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.659 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.659 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.659 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.658 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.658 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 1o97 | FAD | Electron transfer flavoprotein subunit alpha | / | 0.658 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.658 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.658 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.658 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.658 | |
| 4irn | FAD | AnaB | / | 0.658 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.658 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.657 | |
| 3rha | FDA | Putrescine oxidase | / | 0.657 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.657 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.656 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.656 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.656 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.656 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.655 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.655 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.654 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.654 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.652 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.652 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.652 | |
| 4ykf | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.652 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.651 | |
| 3fbs | FAD | Oxidoreductase | / | 0.651 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.651 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.651 | |
| 3w4y | FAD | Mitochondrial FAD-linked sulfhydryl oxidase ERV1 | 1.8.3.2 | 0.651 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.651 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.651 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.651 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.650 | |
| 1um0 | FMN | Chorismate synthase | / | 0.650 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.650 |