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 |
|---|---|---|---|
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 5hsa | FAS | Alcohol oxidase 1 | 1.1.3.13 | 1.285 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.877 | |
| 4z24 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.868 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.855 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.851 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.851 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.846 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.832 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.808 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.790 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.784 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.773 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.770 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.766 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.764 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.762 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.759 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.759 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.753 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.748 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.746 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.746 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.745 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.745 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.744 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.740 | |
| 3lxd | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.740 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.737 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.736 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.736 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.736 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.735 | |
| 1yqz | FAD | Coenzyme A disulfide reductase | / | 0.734 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.734 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.734 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.730 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.729 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.729 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.729 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.729 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.729 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.728 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.723 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.719 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.719 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.718 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.718 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.716 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.716 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.716 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.716 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.715 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.715 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.714 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.714 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.713 | |
| 1ijh | FAD | Cholesterol oxidase | 1.1.3.6 | 0.711 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.711 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.711 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.710 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.710 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.710 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.709 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.707 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.707 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.706 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.706 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.706 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.704 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.704 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.703 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.703 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.703 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.701 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.701 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.700 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.699 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.699 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.699 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.699 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.699 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.698 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.698 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.698 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.697 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.697 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.696 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.696 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.695 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.695 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.694 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.691 | |
| 5a8a | FMN | Riboflavin biosynthesis protein RibF | 2.7.1.26 | 0.691 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.690 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.690 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.689 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.689 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.689 | |
| 2dki | FAD | 3-hydroxybenzoate 4-monooxygenase | 1.14.13.23 | 0.688 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.688 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.688 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.687 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.686 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.686 | |
| 4bjz | FAD | Probable salicylate monooxygenase | / | 0.685 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.685 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.684 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.683 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.683 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.683 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.682 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.682 | |
| 3rha | FDA | Putrescine oxidase | / | 0.682 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.682 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.681 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.680 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.679 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.679 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.679 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.679 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.678 | |
| 2eq8 | FAD | Dihydrolipoyl dehydrogenase | / | 0.678 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.678 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.678 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.678 | |
| 4x4j | FAD | Putative oxygenase | / | 0.678 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.677 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.677 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.677 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.677 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.677 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.676 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.676 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.676 | |
| 4tm1 | FDA | KtzI | / | 0.676 | |
| 2c12 | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.675 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.675 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.675 | |
| 1gaw | FAD | Ferredoxin | / | 0.674 | |
| 4lii | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.674 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.674 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.673 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.673 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.672 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.672 | |
| 4tlz | FAD | KtzI | / | 0.672 | |
| 2j3n | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.671 | |
| 4aox | FAD | Steroid monooxygenase | / | 0.671 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.671 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.671 | |
| 2ym1 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.670 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.669 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.669 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.669 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.669 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.668 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.668 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.667 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.667 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.666 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.666 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.666 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.666 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.666 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.666 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.665 | |
| 4fk1 | FAD | Putative thioredoxin reductase | / | 0.665 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.665 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.664 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.664 | |
| 4txi | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.664 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.663 | |
| 2bab | FAD | Putative aminooxidase | / | 0.663 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.663 | |
| 4d7e | FAD | Putative lysine-N-oxygenase | / | 0.663 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.662 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.662 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.662 | |
| 2ym2 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.662 | |
| 4tlx | FDA | KtzI | / | 0.662 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.661 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.661 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.661 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.661 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.661 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.661 | |
| 2zz0 | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.660 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.660 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.660 | |
| 4o8a | FAD | Bifunctional protein PutA | 1.2.1.88 | 0.660 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.659 | |
| 3gg1 | FMN | Uncharacterized protein | / | 0.659 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.659 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.659 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.659 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.659 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.658 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.658 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.658 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.658 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.657 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.657 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.656 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.656 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.656 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.656 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.656 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.655 | |
| 2bac | FAD | Putative aminooxidase | / | 0.655 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.655 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.655 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.655 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.655 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.655 | |
| 1e1m | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.654 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 0.654 | |
| 4nev | FAD | Trypanothione reductase | / | 0.654 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.653 | |
| 1sez | FAD | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.653 | |
| 1y56 | ATP | Uncharacterized protein | / | 0.653 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.653 | |
| 4emj | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.653 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.653 | |
| 4tm4 | FDA | KtzI | / | 0.653 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.652 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.652 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.652 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.652 | |
| 4o5q | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.652 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.651 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.651 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.651 | |
| 4o5u | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.651 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.650 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.650 | |
| 2bra | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.650 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.650 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.650 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.650 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.650 |