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 |
|---|---|---|---|
| 3nix | FAD | Flavoprotein/dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3nix | FAD | Flavoprotein/dehydrogenase | / | 1.459 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.849 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.841 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.808 | |
| 3grs | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.802 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.801 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.801 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.799 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.797 | |
| 4jn9 | FAD | DepH | / | 0.794 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.789 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.784 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.783 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.778 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.775 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.769 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.767 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.765 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.762 | |
| 4nev | FAD | Trypanothione reductase | / | 0.762 | |
| 4nte | FAD | DepH | / | 0.760 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.757 | |
| 4jy2 | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.757 | |
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.755 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.755 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.754 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.753 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.753 | |
| 4bjz | FAD | Probable salicylate monooxygenase | / | 0.753 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.752 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.750 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.748 | |
| 4kpr | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.746 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.743 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.742 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.741 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.739 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.738 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.738 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.736 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.734 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.729 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.728 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.727 | |
| 4h2p | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.726 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.723 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.722 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.722 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.721 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.720 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.720 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.719 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.716 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.716 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.716 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.715 | |
| 2bac | FAD | Putative aminooxidase | / | 0.713 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.712 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.711 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.711 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.711 | |
| 2eq8 | FAD | Dihydrolipoyl dehydrogenase | / | 0.710 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.710 | |
| 4emj | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.710 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.707 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.707 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.705 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.705 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.703 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.702 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.701 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.701 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.700 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.698 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.698 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.697 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.697 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.697 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.696 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.696 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.695 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.695 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.695 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.694 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.694 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.694 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.694 | |
| 2xyo | FAD | TetX family tetracycline inactivation enzyme | / | 0.693 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.692 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.691 | |
| 1y56 | ATP | Uncharacterized protein | / | 0.691 | |
| 4b66 | FAD | L-ornithine N(5)-monooxygenase | / | 0.690 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.690 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.689 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.689 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.689 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.688 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.688 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.687 | |
| 2ard | FDA | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.687 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.687 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.685 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.685 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.685 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.684 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.684 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.684 | |
| 4tm4 | FDA | KtzI | / | 0.684 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.683 | |
| 2wes | FAD | Tryptophan 5-halogenase | / | 0.683 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.683 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.683 | |
| 4u8p | FDA | UDP-galactopyranose mutase | / | 0.683 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.682 | |
| 3rp8 | FAD | FAD-dependent urate hydroxylase | / | 0.682 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.682 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.682 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.681 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.681 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.681 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.680 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.680 | |
| 3rha | FDA | Putrescine oxidase | / | 0.678 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.678 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.677 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.677 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.677 | |
| 5efw | FMN | NPH1-1 | / | 0.677 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.676 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.676 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.676 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.676 | |
| 3c4a | FAD | Protodeoxyviolaceinate monooxygenase | 1 | 0.676 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.676 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.675 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.675 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.675 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.674 | |
| 4j31 | FAD | Kynurenine 3-monooxygenase | / | 0.674 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.674 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.673 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.673 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.671 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.670 | |
| 2apg | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.669 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.669 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.669 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.669 | |
| 4k5r | FAD | Oxygenase | / | 0.669 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.668 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.668 | |
| 3uth | FDA | UDP-galactopyranose mutase | / | 0.668 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.668 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.668 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.667 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.667 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.667 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.667 | |
| 4icy | FAD | PgaE | / | 0.667 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.666 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.666 | |
| 4x4j | FAD | Putative oxygenase | / | 0.666 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.665 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.665 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.664 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.664 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.663 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.663 | |
| 4j34 | FAD | Kynurenine 3-monooxygenase | / | 0.663 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.663 | |
| 4z2t | FAD | 2-hydroxybiphenyl-3-monooxygenase | / | 0.663 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.662 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.662 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.662 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.662 | |
| 4ykf | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.662 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.661 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.661 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.661 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.660 | |
| 1rx0 | FAD | Isobutyryl-CoA dehydrogenase, mitochondrial | 1.3.99 | 0.659 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.659 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.659 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.659 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.659 | |
| 1gxf | FAD | Trypanothione reductase | 1.8.1.12 | 0.658 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.658 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.658 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.658 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.658 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.657 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.657 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.657 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.657 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.657 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.656 | |
| 2bab | FAD | Putative aminooxidase | / | 0.656 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.656 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.655 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.655 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.655 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.654 | |
| 2tmd | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.654 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.654 | |
| 3fbs | FAD | Oxidoreductase | / | 0.654 | |
| 3ust | FAD | AcMNPV orf92 | / | 0.654 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.653 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.653 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.653 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.652 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.652 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.652 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.652 | |
| 4tm0 | FAD | KtzI | / | 0.652 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.651 | |
| 1o94 | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.651 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.651 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.651 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.651 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.651 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.650 | |
| 2qa1 | FAD | PgaE | / | 0.650 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.650 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.650 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.650 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.650 |