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 |
|---|---|---|---|
| 3ukk | FDA | UDP-galactopyranose mutase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3ukk | FDA | UDP-galactopyranose mutase | / | 1.205 | |
| 4u8p | FDA | UDP-galactopyranose mutase | / | 0.983 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.976 | |
| 3ukl | FAD | UDP-galactopyranose mutase | / | 0.975 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.970 | |
| 3uth | FDA | UDP-galactopyranose mutase | / | 0.958 | |
| 4u8m | FDA | UDP-galactopyranose mutase | / | 0.943 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.931 | |
| 4u8k | FDA | UDP-galactopyranose mutase | / | 0.930 | |
| 4u8j | FDA | UDP-galactopyranose mutase | / | 0.927 | |
| 4u8l | FDA | UDP-galactopyranose mutase | / | 0.921 | |
| 4u8o | FDA | UDP-galactopyranose mutase | / | 0.919 | |
| 4u8n | FDA | UDP-galactopyranose mutase | / | 0.907 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.901 | |
| 3utg | FDA | UDP-galactopyranose mutase | / | 0.897 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.891 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.886 | |
| 3uka | FAD | UDP-galactopyranose mutase | / | 0.867 | |
| 5hhf | FDA | UDP-galactopyranose mutase | / | 0.854 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.849 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.840 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.839 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.822 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.813 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.800 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.791 | |
| 4gdd | FAD | UDP-galactopyranose mutase | / | 0.788 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.783 | |
| 3rha | FDA | Putrescine oxidase | / | 0.782 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.762 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.761 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.756 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.754 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.754 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.751 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.748 | |
| 3m12 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.748 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.747 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.747 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.746 | |
| 3we0 | FAD | Lysine 2-monooxygenase | / | 0.746 | |
| 3ute | FAD | UDP-galactopyranose mutase | / | 0.741 | |
| 2yr4 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.740 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.740 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.739 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.736 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.736 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.736 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.736 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.734 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.734 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.733 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.731 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.731 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.730 | |
| 4cy8 | FDA | 2-hydroxybiphenyl-3-monooxygenase | / | 0.730 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.729 | |
| 1reo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.729 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.729 | |
| 1jnz | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.728 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.728 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.726 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.725 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.725 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.725 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.724 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.723 | |
| 3hdy | FAD | UDP-galactopyranose mutase | / | 0.723 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.722 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.722 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.722 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.720 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.719 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.718 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.718 | |
| 2vou | FAD | 2,6-dihydroxypyridine 3-monooxygenase | 1.14.13.10 | 0.717 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.716 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.715 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.715 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.715 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.715 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.714 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.711 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.710 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.710 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.710 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.709 | |
| 4udr | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.709 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.708 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.707 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.707 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.705 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.704 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.703 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.703 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.702 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.702 | |
| 2yls | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.702 | |
| 2vq7 | FAD | Putative flavin-containing monooxygenase | / | 0.701 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.700 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.699 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.699 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.699 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.699 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.698 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.698 | |
| 1k0j | FAD | p-hydroxybenzoate hydroxylase | / | 0.696 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.696 | |
| 3qj4 | FAD | Renalase | / | 0.696 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.695 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.695 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.695 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.695 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.694 | |
| 1sez | FAD | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.693 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.692 | |
| 4mo2 | FDA | UDP-galactopyranose mutase | / | 0.692 | |
| 1nhs | FAD | NADH peroxidase | 1.11.1.1 | 0.691 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.691 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.691 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.690 | |
| 1d7l | RFL | p-hydroxybenzoate hydroxylase | / | 0.689 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.688 | |
| 4rpj | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.688 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.687 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.687 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.687 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.686 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.685 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.685 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.685 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.684 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.684 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.684 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.683 | |
| 2c4c | FAD | [F-actin]-methionine sulfoxide oxidase MICAL1 | 1.14.13 | 0.683 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.682 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.682 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.682 | |
| 2npx | FAD | NADH peroxidase | 1.11.1.1 | 0.682 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.682 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.682 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.682 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.681 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.681 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.681 | |
| 4j31 | FAD | Kynurenine 3-monooxygenase | / | 0.681 | |
| 4ykf | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.681 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.680 | |
| 1e1l | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.679 | |
| 4ocg | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.679 | |
| 2oal | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.678 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.678 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.677 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.677 | |
| 3dk8 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.675 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.675 | |
| 4k2x | FAD | Polyketide oxygenase/hydroxylase | / | 0.674 | |
| 4rph | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.674 | |
| 1e1m | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.673 | |
| 1y56 | FAD | 382aa long hypothetical sarcosine oxidase | / | 0.673 | |
| 3rnm | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.672 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.672 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.671 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.671 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.671 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.671 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.670 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.670 | |
| 2oa1 | FAD | Flavin-dependent tryptophan halogenase RebH | 1.14.19.9 | 0.669 | |
| 3kkj | FAD | Renalase | / | 0.669 | |
| 3znp | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.669 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.668 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.668 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.668 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.668 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.667 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.667 | |
| 4x4j | FAD | Putative oxygenase | / | 0.667 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.666 | |
| 4tm0 | FAD | KtzI | / | 0.666 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.665 | |
| 2ar8 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.664 | |
| 3t14 | FAD | Sulfide-quinone reductase | / | 0.664 | |
| 2bab | FAD | Putative aminooxidase | / | 0.663 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.663 | |
| 4z44 | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.663 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.662 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.662 | |
| 3itj | FAD | Thioredoxin reductase 1 | 1.8.1.9 | 0.662 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.660 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.660 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.660 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.660 | |
| 3k4n | FAD | Pyranose 2-oxidase | / | 0.659 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.659 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.659 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.659 | |
| 2qa1 | FAD | PgaE | / | 0.657 | |
| 3t2y | FAD | Sulfide-quinone reductase | / | 0.657 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.656 | |
| 1gal | FAD | Glucose oxidase | 1.1.3.4 | 0.656 | |
| 2gvc | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.656 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.656 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.656 | |
| 3nt6 | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.655 | |
| 3syi | FAD | Sulfide-quinone reductase | / | 0.655 | |
| 4usr | FAD | Monooxygenase | / | 0.655 | |
| 2bac | FAD | Putative aminooxidase | / | 0.654 | |
| 1nhq | FAD | NADH peroxidase | 1.11.1.1 | 0.653 | |
| 1zx9 | FAD | Mercuric reductase | 1.16.1.1 | 0.653 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.653 | |
| 2rab | FAD | Glutathione amide reductase | / | 0.653 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.653 | |
| 2yvf | FAD | Ferredoxin reductase | / | 0.653 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.653 | |
| 4hb9 | FAD | Uncharacterized protein | / | 0.652 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.651 | |
| 2cdu | FAD | NADH oxidase | / | 0.651 | |
| 1c0l | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.650 | |
| 4gdc | FAD | UDP-galactopyranose mutase | / | 0.650 |