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 |
|---|---|---|---|
| 3hjk | FAD | Vivid PAS protein VVD |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.557 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.479 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.469 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.389 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 1.365 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.315 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.060 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.040 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.038 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.028 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.027 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.985 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.971 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.968 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.951 | |
| 4hia | FMN | LOV protein | / | 0.949 | |
| 2v1a | FMN | NPH1-1 | / | 0.948 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.941 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.938 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.937 | |
| 2v0u | FMN | NPH1-1 | / | 0.931 | |
| 5djt | FMN | NPH1-2 | / | 0.923 | |
| 5efw | FMN | NPH1-1 | / | 0.918 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.915 | |
| 5dju | FMN | NPH1-2 | / | 0.898 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.897 | |
| 3sw1 | FMN | Sensory box protein | / | 0.865 | |
| 4hnb | FMN | LOV protein | / | 0.861 | |
| 4hj4 | FMN | LOV protein | / | 0.860 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.860 | |
| 4wf0 | FMN | NPH1-1 | / | 0.858 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.851 | |
| 4hj6 | FMN | LOV protein | / | 0.839 | |
| 5j4e | FMN | Sensory box protein | / | 0.834 | |
| 5j3w | FMN | Sensory box protein | / | 0.820 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.816 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.800 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.783 | |
| 1g28 | FMN | PHY3 | / | 0.767 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.759 | |
| 4hj3 | FMN | LOV protein | / | 0.754 | |
| 5cho | FAD | Flavin reductase | / | 0.725 | |
| 5dkk | FMN | Predicted protein | / | 0.725 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.719 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.718 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.716 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.711 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.709 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.709 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.708 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.701 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.696 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.694 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.693 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.693 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.692 | |
| 3i99 | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.692 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.691 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.689 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.687 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.686 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.686 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.686 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.685 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.684 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.684 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 4irn | FAD | AnaB | / | 0.683 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.683 | |
| 2ed4 | FAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.682 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.682 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.682 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.682 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.681 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.681 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.680 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.680 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.679 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.679 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.678 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.678 | |
| 5ahs | FAD | Acyl-CoA dehydrogenase | / | 0.678 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.677 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.676 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.676 | |
| 1t6z | RBF | Riboflavin biosynthesis protein | / | 0.676 | |
| 4bjz | FAD | Probable salicylate monooxygenase | / | 0.676 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.676 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.675 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.674 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.674 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.674 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.673 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.673 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.672 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.672 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.672 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.672 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.672 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.671 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.671 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.671 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.670 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.670 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.670 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.668 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.668 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.668 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.668 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.667 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.667 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.667 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.666 | |
| 3pft | FMN | Flavin reductase | / | 0.665 | |
| 1h7w | FMN | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.664 | |
| 1kyv | RBF | 6,7-dimethyl-8-ribityllumazine synthase | 2.5.1.78 | 0.664 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.664 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.664 | |
| 3ae4 | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.663 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.663 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.662 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.662 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.662 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.662 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.661 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.660 | |
| 1p0n | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.660 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.659 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.658 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.658 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.658 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.658 | |
| 1n07 | FMN | Riboflavin kinase | 2.7.1.26 | 0.657 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 1rz1 | FAD | Phenol 2-hydroxylase component B | / | 0.657 | |
| 2vxa | RBF | Dodecin | / | 0.657 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.657 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.657 | |
| 4z9r | FMN | Omega-3 polyunsaturated fatty acid synthase subunit PfaD | / | 0.657 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.656 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.656 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.656 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.655 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.655 | |
| 4j8p | FMN | Flavodoxin | / | 0.655 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 4bmo | FMN | Protein NrdI | / | 0.653 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.653 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.653 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.653 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.652 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.652 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.652 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.652 | |
| 2pan | FAD | Glyoxylate carboligase | 4.1.1.47 | 0.651 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.651 | |
| 3n39 | FMN | Protein NrdI | / | 0.651 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.651 | |
| 3kkj | FAD | Renalase | / | 0.650 |