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 |
|---|---|---|---|
| 1n9l | FMN | Putative blue light receptor |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1n9l | FMN | Putative blue light receptor | / | 1.312 | |
| 1n9n | FMN | Putative blue light receptor | / | 1.227 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 1.076 | |
| 5efw | FMN | NPH1-1 | / | 1.052 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 1.016 | |
| 2v1a | FMN | NPH1-1 | / | 0.995 | |
| 5dju | FMN | NPH1-2 | / | 0.994 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.985 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.979 | |
| 3d72 | FAD | Vivid PAS protein VVD | / | 0.969 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.965 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.964 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 0.963 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.956 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 0.952 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.946 | |
| 4hia | FMN | LOV protein | / | 0.944 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.937 | |
| 2v0u | FMN | NPH1-1 | / | 0.936 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.935 | |
| 5djt | FMN | NPH1-2 | / | 0.924 | |
| 5j3w | FMN | Sensory box protein | / | 0.911 | |
| 4hj3 | FMN | LOV protein | / | 0.900 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.897 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 0.896 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.894 | |
| 4hj6 | FMN | LOV protein | / | 0.881 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.880 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.878 | |
| 4wf0 | FMN | NPH1-1 | / | 0.876 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.874 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.869 | |
| 4hnb | FMN | LOV protein | / | 0.861 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.853 | |
| 4hj4 | FMN | LOV protein | / | 0.792 | |
| 3sw1 | FMN | Sensory box protein | / | 0.737 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.737 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.736 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.722 | |
| 1g28 | FMN | PHY3 | / | 0.719 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.714 | |
| 3bnk | FMN | Flavoredoxin | / | 0.713 | |
| 1usc | FMN | Monooxygenase | / | 0.710 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.709 | |
| 5cho | FAD | Flavin reductase | / | 0.707 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.703 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.701 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.701 | |
| 2iyi | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.700 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.699 | |
| 1efp | FAD | Electron transfer flavoprotein subunit alpha | / | 0.698 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.698 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.698 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.697 | |
| 5j4e | FMN | Sensory box protein | / | 0.697 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.695 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.695 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.694 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.694 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.694 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.691 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.689 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.689 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.689 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.689 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.688 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.688 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.686 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.686 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.686 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.685 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.683 | |
| 2g37 | FAD | Proline dehydrogenase | / | 0.683 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.683 | |
| 2iyg | FMN | AppA, antirepressor of ppsR, sensor of blue light | / | 0.682 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.682 | |
| 4zoh | FAD | Putative oxidoreductase FAD-binding subunit | / | 0.682 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.681 | |
| 1gaq | FAD | Ferredoxin | / | 0.681 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.681 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.681 | |
| 2vxa | RBF | Dodecin | / | 0.680 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.679 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.679 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.679 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.679 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.679 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.679 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.679 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.679 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.678 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.677 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.677 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.677 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.677 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.677 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.676 | |
| 4k5r | FAD | Oxygenase | / | 0.676 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.676 | |
| 1efv | FAD | Electron transfer flavoprotein subunit alpha, mitochondrial | / | 0.675 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.675 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.675 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.674 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.674 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.673 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.673 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.673 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.672 | |
| 1vcf | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.672 | |
| 3fsu | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.672 | |
| 4e2d | FMN | Dehydrogenase | / | 0.672 | |
| 4nev | FAD | Trypanothione reductase | / | 0.672 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.671 | |
| 3n3b | FMN | Protein NrdI | / | 0.671 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.670 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.670 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.670 | |
| 3n3a | FMN | Protein NrdI | / | 0.670 | |
| 5dkk | FMN | Predicted protein | / | 0.670 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.669 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 4jay | FAD | UDP-N-acetylenolpyruvoylglucosamine reductase | / | 0.669 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.668 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.668 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.668 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.668 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.667 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.666 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.666 | |
| 1zp3 | FAD | 5,10-methylenetetrahydrofolate reductase | 1.5.1.20 | 0.666 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.665 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.664 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.664 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.664 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.663 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.662 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.662 | |
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 0.662 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.661 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.660 | |
| 1eje | FMN | Protein MTH_152 | / | 0.659 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.659 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.659 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.659 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.659 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.659 | |
| 1dor | FMN | Dihydroorotate dehydrogenase A (fumarate) | 1.3.98.1 | 0.658 | |
| 2a1t | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.658 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.658 | |
| 3aeb | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.657 | |
| 3gfy | FMN | Uncharacterized protein | / | 0.657 | |
| 3rp8 | FAD | FAD-dependent urate hydroxylase | / | 0.657 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.657 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.657 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.656 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.656 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.656 | |
| 2iml | FMN | Uncharacterized protein | / | 0.656 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.655 | |
| 3k7t | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.655 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.653 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.653 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.652 | |
| 2qmy | FAD | Ribosyldihydronicotinamide dehydrogenase [quinone] | / | 0.651 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.651 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.651 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.650 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.650 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.650 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.650 | |
| 4e2b | FMN | Dehydrogenase | / | 0.650 |