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 |
|---|---|---|---|
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3g5q | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 1.427 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 1.403 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.862 | |
| 3grs | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.859 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.857 | |
| 1bwc | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.837 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.836 | |
| 4gr1 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.826 | |
| 1rp0 | AHZ | Thiamine thiazole synthase, chloroplastic | / | 0.811 | |
| 1ges | FAD | Glutathione reductase | 1.8.1.7 | 0.807 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.806 | |
| 2q0l | FAD | Thioredoxin reductase | 1.8.1.9 | 0.805 | |
| 2wow | FAD | Trypanothione reductase | / | 0.799 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.794 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.793 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.787 | |
| 2eq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.784 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.783 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.778 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.776 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.775 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.774 | |
| 1ojt | FAD | Dihydrolipoyl dehydrogenase | / | 0.764 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.763 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.763 | |
| 2r9z | FAD | Glutathione amide reductase | / | 0.763 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.761 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.761 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.757 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.757 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.756 | |
| 2x8g | FAD | Thioredoxin glutathione reductase | / | 0.752 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.752 | |
| 1ger | FAD | Glutathione reductase | 1.8.1.7 | 0.750 | |
| 2v6o | FAD | Thioredoxin glutathione reductase | / | 0.750 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.750 | |
| 2ylx | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.748 | |
| 1feb | FAD | Trypanothione reductase | 1.8.1.12 | 0.747 | |
| 5eow | FAD | 6-hydroxynicotinate 3-monooxygenase | 1.14.13.114 | 0.747 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.746 | |
| 2rgj | FAD | Flavin-containing monooxygenase | / | 0.745 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.742 | |
| 1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.741 | |
| 1pdh | FAS | p-hydroxybenzoate hydroxylase | / | 0.739 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.739 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.737 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.735 | |
| 3jsk | AHZ | Thiamine thiazole synthase | / | 0.733 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.731 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.730 | |
| 4kpr | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.729 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.728 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.726 | |
| 4em4 | FAD | Coenzyme A disulfide reductase | / | 0.726 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.726 | |
| 3l8k | ADP | Dihydrolipoamide dehydrogenase (PdhD-3) | / | 0.724 | |
| 1lpf | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.722 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.722 | |
| 3k30 | ADP | Histamine dehydrogenase | / | 0.722 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.720 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.720 | |
| 1npx | FAD | NADH peroxidase | 1.11.1.1 | 0.720 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.719 | |
| 4j57 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.719 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.718 | |
| 4b63 | FAD | L-ornithine N(5)-monooxygenase | / | 0.716 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.714 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.714 | |
| 2jib | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.714 | |
| 1k0l | FAD | p-hydroxybenzoate hydroxylase | / | 0.712 | |
| 2eq7 | NAD | Dihydrolipoyl dehydrogenase | / | 0.712 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.711 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.711 | |
| 5dbj | FAD | FADH2-dependent halogenase PltA | / | 0.711 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.711 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.709 | |
| 4tm4 | FDA | KtzI | / | 0.709 | |
| 5cku | FAD | L-ornithine N(5)-monooxygenase | / | 0.709 | |
| 3ada | NAD | Subunit alpha of sarocosine oxidase | / | 0.708 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.704 | |
| 3lad | FAD | Dihydrolipoyl dehydrogenase | / | 0.703 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.702 | |
| 2dki | FAD | 3-hydroxybenzoate 4-monooxygenase | 1.14.13.23 | 0.701 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.701 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.701 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.700 | |
| 1djn | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.699 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.698 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.698 | |
| 3rp8 | FAD | FAD-dependent urate hydroxylase | / | 0.698 | |
| 2hqm | FAD | Glutathione reductase | 1.8.1.7 | 0.695 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.695 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.695 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.694 | |
| 2tmd | ADP | Trimethylamine dehydrogenase | 1.5.8.2 | 0.694 | |
| 1e1m | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.692 | |
| 4eqw | FAD | Coenzyme A disulfide reductase | / | 0.692 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.692 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.692 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.691 | |
| 4ap3 | FAD | Steroid monooxygenase | / | 0.690 | |
| 4d7e | FAD | Putative lysine-N-oxygenase | / | 0.690 | |
| 4eqr | FAD | Coenzyme A disulfide reductase | / | 0.690 | |
| 4tm3 | FAD | KtzI | / | 0.690 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.690 | |
| 4b64 | FAD | L-ornithine N(5)-monooxygenase | / | 0.688 | |
| 4nzh | FAD | L-ornithine N(5)-monooxygenase | / | 0.688 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.687 | |
| 4tm1 | FDA | KtzI | / | 0.687 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.686 | |
| 1lvl | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.683 | |
| 2qae | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.683 | |
| 3kkj | FAD | Renalase | / | 0.682 | |
| 1yqz | FAD | Coenzyme A disulfide reductase | / | 0.681 | |
| 2eq6 | FAD | Dihydrolipoyl dehydrogenase | / | 0.681 | |
| 2gsd | NAD | Formate dehydrogenase | / | 0.680 | |
| 4eqs | FAD | Coenzyme A disulfide reductase | / | 0.680 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.680 | |
| 1grh | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.679 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.679 | |
| 5js6 | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.679 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.678 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.677 | |
| 4eqx | FAD | Coenzyme A disulfide reductase | / | 0.677 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.676 | |
| 2vqb | FAD | Putative flavin-containing monooxygenase | / | 0.676 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.676 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.676 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.675 | |
| 4ap1 | FAD | Steroid monooxygenase | / | 0.674 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.673 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.672 | |
| 2x3n | FAD | Probable FAD-dependent monooxygenase | / | 0.672 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.672 | |
| 4txi | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.672 | |
| 2qa2 | FAD | Polyketide oxygenase CabE | / | 0.671 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.671 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.671 | |
| 3qvw | NAD | Myo-inositol-1-phosphate synthase (Ino1) | / | 0.671 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.671 | |
| 1sc6 | NAD | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.670 | |
| 2qa1 | FAD | PgaE | / | 0.669 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.669 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.668 | |
| 5bp7 | SAH | SAM-dependent methyltransferase | / | 0.668 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.667 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.667 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.667 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.666 | |
| 3lxd | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.666 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.665 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.665 | |
| 3s5w | FAD | L-ornithine N(5)-monooxygenase | / | 0.665 | |
| 1grg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.664 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.664 | |
| 1w4x | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.664 | |
| 3pqf | NAD | L-lactate dehydrogenase | 1.1.1.27 | 0.664 | |
| 2cdu | ADP | NADH oxidase | / | 0.663 | |
| 3x2f | NAI | Adenosylhomocysteinase | / | 0.663 | |
| 4d04 | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.663 | |
| 4b67 | FAD | L-ornithine N(5)-monooxygenase | / | 0.662 | |
| 2ylz | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.661 | |
| 5hhf | FDA | UDP-galactopyranose mutase | / | 0.661 | |
| 1f8w | FAD | NADH peroxidase | 1.11.1.1 | 0.660 | |
| 1zmc | NAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.660 | |
| 4rdi | ATP | tRNA threonylcarbamoyladenosine dehydratase | 6.1 | 0.660 | |
| 4p8r | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.659 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.659 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.659 | |
| 5jsf | NAD | 17-beta-hydroxysteroid dehydrogenase 14 | 1.1.1 | 0.659 | |
| 2ji7 | ADP | Oxalyl-CoA decarboxylase | 4.1.1.8 | 0.658 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.657 | |
| 3wv8 | ATP | Hmd co-occurring protein HcgE | / | 0.657 | |
| 1grb | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.656 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.656 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.656 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.656 | |
| 1mxt | FAE | Cholesterol oxidase | 1.1.3.6 | 0.655 | |
| 3ics | ADP | Coenzyme A disulfide reductase | / | 0.655 | |
| 4jn9 | FAD | DepH | / | 0.655 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1jki | NAI | Inositol-3-phosphate synthase | 5.5.1.4 | 0.653 | |
| 1szj | NAD | Glyceraldehyde-3-phosphate dehydrogenase | 1.2.1.12 | 0.653 | |
| 4fx9 | FAD | Coenzyme A disulfide reductase | 1.8.1.14 | 0.653 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.652 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.652 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.652 | |
| 3alj | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.652 | |
| 3ihg | FAD | Aklavinone 12-hydroxylase RdmE | / | 0.652 | |
| 3t2k | FAD | Sulfide-quinone reductase | / | 0.652 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.651 | |
| 3djg | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.651 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.651 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.651 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.651 | |
| 4ocg | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.651 | |
| 2plw | SAM | Ribosomal RNA methyltransferase, putative | / | 0.650 | |
| 3wle | NAD | (R)-specific carbonyl reductase | / | 0.650 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.650 |