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 |
|---|---|---|---|
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3alm | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.341 | |
| 4jy2 | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.167 | |
| 4h2n | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.155 | |
| 4h2p | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.118 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.116 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.086 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 1.055 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.891 | |
| 4bjz | FAD | Probable salicylate monooxygenase | / | 0.886 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.867 | |
| 4k5r | FAD | Oxygenase | / | 0.859 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.840 | |
| 2qa1 | FAD | PgaE | / | 0.834 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.815 | |
| 4j34 | FAD | Kynurenine 3-monooxygenase | / | 0.815 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.812 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.812 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.807 | |
| 3rp8 | FAD | FAD-dependent urate hydroxylase | / | 0.791 | |
| 1d7l | RFL | p-hydroxybenzoate hydroxylase | / | 0.788 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.788 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.785 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.783 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.782 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.779 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.778 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.777 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.773 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.768 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.764 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.763 | |
| 4j31 | FAD | Kynurenine 3-monooxygenase | / | 0.762 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.757 | |
| 3c4a | FAD | Protodeoxyviolaceinate monooxygenase | 1 | 0.757 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.757 | |
| 3nix | FAD | Flavoprotein/dehydrogenase | / | 0.755 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.755 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.755 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.751 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.750 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.748 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.748 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.747 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.746 | |
| 4a6n | FAD | TetX family tetracycline inactivation enzyme | / | 0.745 | |
| 4m52 | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.745 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.744 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.743 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.743 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.743 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.743 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.741 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.739 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.738 | |
| 2eq8 | FAD | Dihydrolipoyl dehydrogenase | / | 0.734 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.733 | |
| 1phh | FAD | p-hydroxybenzoate hydroxylase | / | 0.732 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.730 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.729 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.726 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.726 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.726 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.725 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.724 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.724 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.723 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.722 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.722 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.721 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.720 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.718 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.716 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.715 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.715 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.712 | |
| 3grs | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.712 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.711 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.711 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.710 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.708 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.708 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.707 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.706 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.706 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.706 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.706 | |
| 4x4j | FAD | Putative oxygenase | / | 0.705 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.703 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.702 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.700 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.699 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.699 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.699 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.699 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.699 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.697 | |
| 4icy | FAD | PgaE | / | 0.697 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.696 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.695 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.695 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.694 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.694 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.694 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.693 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.693 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.693 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.691 | |
| 1geu | FAD | Glutathione reductase | 1.8.1.7 | 0.690 | |
| 2fjb | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.690 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.689 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.689 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.689 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.688 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.686 | |
| 4jn9 | FAD | DepH | / | 0.686 | |
| 2bac | FAD | Putative aminooxidase | / | 0.685 | |
| 2nvk | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.685 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.685 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.684 | |
| 2bab | FAD | Putative aminooxidase | / | 0.684 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.684 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.683 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.683 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.683 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.682 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.681 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.681 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.680 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.680 | |
| 4nte | FAD | DepH | / | 0.680 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.679 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.679 | |
| 3lxd | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.679 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.678 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.678 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.678 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.678 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.678 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.678 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.678 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.677 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.677 | |
| 2wba | FAD | Trypanothione reductase | 1.8.1.12 | 0.676 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.676 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.676 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.676 | |
| 1fec | FAD | Trypanothione reductase | 1.8.1.12 | 0.675 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.674 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.674 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.672 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.672 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.672 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.672 | |
| 1lpf | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.671 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.671 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.671 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.671 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.670 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.670 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.670 | |
| 3a27 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.669 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.668 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.667 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.667 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.667 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.667 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.667 | |
| 1h6v | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.666 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.666 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.666 | |
| 4nev | FAD | Trypanothione reductase | / | 0.666 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.665 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.664 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.664 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.664 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.662 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.662 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.662 | |
| 1bzl | FAD | Trypanothione reductase | 1.8.1.12 | 0.661 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.661 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.660 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.660 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.660 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.660 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 2i9k | SAH | Modification methylase HhaI | 2.1.1.37 | 0.659 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.659 | |
| 4guv | FAD | TetX family tetracycline inactivation enzyme | / | 0.658 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.657 | |
| 2o06 | MTA | Spermidine synthase | 2.5.1.16 | 0.657 | |
| 2z6u | SAH | Modification methylase HhaI | 2.1.1.37 | 0.657 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.657 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.657 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.657 | |
| 2c7q | SAH | Modification methylase HhaI | 2.1.1.37 | 0.656 | |
| 2ih2 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.656 | |
| 2np6 | NEA | Modification methylase TaqI | 2.1.1.72 | 0.656 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.656 | |
| 2yxl | SFG | 450aa long hypothetical fmu protein | / | 0.655 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.655 | |
| 7mht | SAH | Modification methylase HhaI | 2.1.1.37 | 0.655 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.654 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.654 | |
| 1q1w | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.654 | |
| 3lb8 | FAD | Putidaredoxin reductase | 1.18.1.5 | 0.654 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.653 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.653 | |
| 4xq6 | FMN | Dihydroorotate dehydrogenase (quinone) | / | 0.653 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.652 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.652 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.652 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.652 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.651 | |
| 3g07 | SAM | 7SK snRNA methylphosphate capping enzyme | 2.1.1 | 0.651 | |
| 4c03 | SFG | Protein arginine N-methyltransferase 6 | / | 0.651 | |
| 4c04 | SFG | Protein arginine N-methyltransferase 6 | / | 0.651 | |
| 4dna | FAD | Probable glutathione reductase | / | 0.651 | |
| 4emj | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.651 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.650 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.650 | |
| 2wow | FAD | Trypanothione reductase | / | 0.650 | |
| 3grr | SAH | Probable ribosomal RNA small subunit methyltransferase A | / | 0.650 | |
| 5fs8 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.650 |