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 |
|---|---|---|---|
| 3s5w | FAD | L-ornithine N(5)-monooxygenase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 1.274 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.991 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.907 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.895 | |
| 4b65 | FAD | L-ornithine N(5)-monooxygenase | / | 0.892 | |
| 4b66 | FAD | L-ornithine N(5)-monooxygenase | / | 0.876 | |
| 4b69 | FAD | L-ornithine N(5)-monooxygenase | / | 0.838 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.831 | |
| 4tm1 | FDA | KtzI | / | 0.831 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.824 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.821 | |
| 4tlx | FDA | KtzI | / | 0.820 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.815 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.789 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.781 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.780 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.776 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.774 | |
| 4tm0 | FAD | KtzI | / | 0.773 | |
| 4x4j | FAD | Putative oxygenase | / | 0.771 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.766 | |
| 4fx9 | FAD | Coenzyme A disulfide reductase | 1.8.1.14 | 0.765 | |
| 4tm3 | FAD | KtzI | / | 0.765 | |
| 4txi | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.762 | |
| 1dnc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.752 | |
| 4tm4 | FDA | KtzI | / | 0.751 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.750 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.744 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.743 | |
| 3up4 | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.742 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.739 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.737 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.735 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.731 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.731 | |
| 1zk7 | FAD | Mercuric reductase | 1.16.1.1 | 0.729 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.728 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.728 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.727 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.725 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.723 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.720 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.716 | |
| 2xdo | FAD | TetX family tetracycline inactivation enzyme | / | 0.715 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.714 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.712 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.711 | |
| 3ukl | FAD | UDP-galactopyranose mutase | / | 0.710 | |
| 4d03 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.710 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.708 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.708 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.707 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.707 | |
| 5hhf | FDA | UDP-galactopyranose mutase | / | 0.707 | |
| 1gre | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.706 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.706 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.706 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.706 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.706 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.705 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.705 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.705 | |
| 4icy | FAD | PgaE | / | 0.704 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.702 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.702 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.701 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.701 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.700 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.700 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.699 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.698 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.698 | |
| 3rha | FDA | Putrescine oxidase | / | 0.698 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.697 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.695 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.695 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.695 | |
| 2ylt | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.695 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.695 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.694 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.693 | |
| 3dk4 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.692 | |
| 3rp8 | FAD | FAD-dependent urate hydroxylase | / | 0.692 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.692 | |
| 1y56 | ATP | Uncharacterized protein | / | 0.690 | |
| 2q28 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.690 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.690 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.690 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.689 | |
| 1gsn | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.689 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.689 | |
| 1e1m | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.688 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.688 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.688 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.688 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.688 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.687 | |
| 1k4q | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.686 | |
| 3uka | FAD | UDP-galactopyranose mutase | / | 0.686 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.686 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.685 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.685 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.685 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.684 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.683 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.683 | |
| 2ji9 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.682 | |
| 3dme | FAD | Putative conserved exported protein | / | 0.682 | |
| 3grs | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.682 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.682 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.682 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.682 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.681 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.681 | |
| 1y8q | ATP | SUMO-activating enzyme subunit 2 | 6.3.2 | 0.681 | |
| 2r0c | FAD | Putative FAD-monooxygenase | / | 0.681 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.681 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.680 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.680 | |
| 4a99 | FAD | TetX family tetracycline inactivation enzyme | / | 0.680 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.680 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.679 | |
| 1i9g | SAM | tRNA (adenine(58)-N(1))-methyltransferase TrmI | / | 0.678 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.678 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.678 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.677 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.677 | |
| 3c96 | FAD | Flavin-containing monooxygenase | / | 0.677 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.677 | |
| 2bac | FAD | Putative aminooxidase | / | 0.676 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.675 | |
| 1gra | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.675 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.675 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.675 | |
| 4yac | NAI | C alpha-dehydrogenase | / | 0.675 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.674 | |
| 2xvh | FAD | Putative flavin-containing monooxygenase | / | 0.674 | |
| 4pyo | SAH | Catechol O-methyltransferase | 2.1.1.6 | 0.674 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.674 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.673 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.673 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.673 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.673 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.673 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.673 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.672 | |
| 2eq8 | FAD | Dihydrolipoyl dehydrogenase | / | 0.672 | |
| 3grv | ADN | Probable ribosomal RNA small subunit methyltransferase A | / | 0.672 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.672 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.671 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.671 | |
| 4k5r | FAD | Oxygenase | / | 0.671 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.670 | |
| 4aox | FAD | Steroid monooxygenase | / | 0.670 | |
| 4iv8 | SAM | Phosphoethanolamine N-methyltransferase,putative | / | 0.670 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.669 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.669 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.669 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.668 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.667 | |
| 1p1i | NAD | Inositol-3-phosphate synthase | 5.5.1.4 | 0.667 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.667 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.667 | |
| 3sqp | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.667 | |
| 3uov | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.667 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.667 | |
| 4ysh | FAD | Glycine oxidase | / | 0.667 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.666 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.666 | |
| 3m12 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.666 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.666 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.666 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.665 | |
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.665 | |
| 5fs8 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.665 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.664 | |
| 2cdu | ADP | NADH oxidase | / | 0.664 | |
| 3p9u | FAD | TetX family tetracycline inactivation enzyme | / | 0.664 | |
| 4bk2 | FAD | Probable salicylate monooxygenase | / | 0.664 | |
| 4yuz | S4M | Spermidine synthase, putative | / | 0.664 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.663 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.663 | |
| 4la1 | FAD | Thioredoxin glutathione reductase | / | 0.663 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.663 | |
| 1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.662 | |
| 3dk9 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.662 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.662 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.661 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.661 | |
| 1djn | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.660 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.660 | |
| 2qa1 | FAD | PgaE | / | 0.660 | |
| 3fpz | AHZ | Thiamine thiazole synthase | / | 0.660 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.660 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.660 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.660 | |
| 3dh9 | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.659 | |
| 4kvz | SAH | PtnL protein | / | 0.659 | |
| 2w0h | FAD | Trypanothione reductase | / | 0.658 | |
| 3h5n | ATP | MccB protein | / | 0.658 | |
| 3uoy | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.658 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.658 | |
| 4u8n | FDA | UDP-galactopyranose mutase | / | 0.658 | |
| 2dki | FAD | 3-hydroxybenzoate 4-monooxygenase | 1.14.13.23 | 0.657 | |
| 3ean | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.657 | |
| 3ids | NAD | Glyceraldehyde-3-phosphate dehydrogenase, glycosomal | 1.2.1.12 | 0.657 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.657 | |
| 3ntd | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.657 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.656 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.656 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.656 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.656 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.655 | |
| 2ji6 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.655 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.655 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.655 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.654 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.654 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.654 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.654 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.654 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.653 | |
| 3kkj | FAD | Renalase | / | 0.653 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.653 | |
| 3ou6 | SAM | SAM-dependent methyltransferase | / | 0.653 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.652 | |
| 3atq | FDA | Conserved Archaeal protein | / | 0.652 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.652 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.652 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.651 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.651 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.651 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.651 | |
| 2ba9 | FAD | Putative aminooxidase | / | 0.650 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.650 | |
| 2ylr | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.650 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.650 | |
| 3nn6 | FB0 | 6-hydroxy-L-nicotine oxidase | / | 0.650 | |
| 4emw | FAD | Coenzyme A disulfide reductase | / | 0.650 | |
| 4hc4 | SAH | Protein arginine N-methyltransferase 6 | / | 0.650 |