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 |
|---|---|---|---|
| 3itj | FAD | Thioredoxin reductase 1 | 1.8.1.9 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3itj | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 1.220 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.948 | |
| 4cbq | FAD | Thioredoxin reductase | / | 0.913 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.893 | |
| 4jnq | FDA | Thioredoxin reductase | / | 0.888 | |
| 3d8x | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.875 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.874 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.868 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.862 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.859 | |
| 4ccr | FAD | Thioredoxin reductase | / | 0.841 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.838 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.827 | |
| 4a65 | FAD | Thioredoxin reductase | / | 0.825 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.821 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.820 | |
| 4nte | FAD | DepH | / | 0.799 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.798 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.781 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.781 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.780 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.775 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.775 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.774 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.774 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.773 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.771 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.768 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.765 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.764 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.763 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.763 | |
| 2cfy | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.760 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.759 | |
| 3fbs | FAD | Oxidoreductase | / | 0.755 | |
| 1fec | FAD | Trypanothione reductase | 1.8.1.12 | 0.752 | |
| 4jn9 | FAD | DepH | / | 0.752 | |
| 3grs | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.751 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.750 | |
| 3lad | FAD | Dihydrolipoyl dehydrogenase | / | 0.749 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.746 | |
| 2wba | FAD | Trypanothione reductase | 1.8.1.12 | 0.746 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.746 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.743 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.743 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.742 | |
| 1zmd | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.740 | |
| 4nev | FAD | Trypanothione reductase | / | 0.740 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.738 | |
| 1typ | FAD | Trypanothione reductase | 1.8.1.12 | 0.737 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.737 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.736 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.735 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.735 | |
| 1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.734 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.734 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.733 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.732 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.732 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.732 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.728 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.727 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.726 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.725 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.725 | |
| 2wow | FAD | Trypanothione reductase | / | 0.725 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.724 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.723 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.722 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.722 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.721 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.720 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.719 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.719 | |
| 1lpf | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.718 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.717 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.716 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.716 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.716 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.715 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.713 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.713 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.712 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.711 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.711 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.711 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.710 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.710 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.709 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.708 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.708 | |
| 2bab | FAD | Putative aminooxidase | / | 0.707 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.707 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.705 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.704 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.704 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.703 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.703 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.702 | |
| 4o5q | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.702 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.701 | |
| 4kpr | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.701 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.700 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.700 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.699 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.698 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.698 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.698 | |
| 1gxf | FAD | Trypanothione reductase | 1.8.1.12 | 0.697 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.697 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.697 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.697 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.696 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.695 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.695 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.693 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.692 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.691 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.691 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.691 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.690 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.689 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.689 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.689 | |
| 4o5u | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.689 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.688 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.688 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.686 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.684 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.684 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.684 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.683 | |
| 2a87 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.683 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.682 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.682 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.682 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.680 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.680 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.679 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.679 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.679 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.678 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.678 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.677 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.676 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.676 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.676 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.675 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.675 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.675 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.674 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.674 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.674 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.674 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.674 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.673 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.672 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.672 | |
| 1bzl | FAD | Trypanothione reductase | 1.8.1.12 | 0.671 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.671 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.671 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.670 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.670 | |
| 3qfb | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.670 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.669 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.669 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.668 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.668 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.667 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.667 | |
| 3f8p | NAD | NADH oxidase/thioredoxin reductase | / | 0.667 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.667 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.666 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.665 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.665 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.665 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.665 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.664 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.664 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.664 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.664 | |
| 3rha | FDA | Putrescine oxidase | / | 0.664 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.663 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.663 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.662 | |
| 3ukk | FDA | UDP-galactopyranose mutase | / | 0.662 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.661 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.661 | |
| 2bac | FAD | Putative aminooxidase | / | 0.660 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.658 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.658 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.658 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.658 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.658 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.657 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.657 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.657 | |
| 2qa1 | FAD | PgaE | / | 0.656 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.656 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.656 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.656 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.655 | |
| 2gr0 | FAD | Ferredoxin reductase | / | 0.655 | |
| 4h4p | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.655 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.655 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.655 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.654 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.654 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.654 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.654 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.653 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.653 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.653 | |
| 1yy5 | FAD | Polyamine oxidase FMS1 | / | 0.652 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.652 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.652 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.652 | |
| 4ysh | FAD | Glycine oxidase | / | 0.652 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.652 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.651 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 0.651 | |
| 3fmw | FAD | Oxygenase | / | 0.651 | |
| 4emj | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.651 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.650 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.650 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.650 |