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 |
|---|---|---|---|
| 3hdy | FDA | UDP-galactopyranose mutase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3hdy | FDA | UDP-galactopyranose mutase | / | 1.236 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 1.009 | |
| 3he3 | FAD | UDP-galactopyranose mutase | / | 0.951 | |
| 3hdy | FAD | UDP-galactopyranose mutase | / | 0.944 | |
| 3kyb | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.816 | |
| 1e6e | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.786 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.780 | |
| 4mo2 | FAD | UDP-galactopyranose mutase | / | 0.774 | |
| 4gcm | FAD | Thioredoxin reductase | 1.8.1.9 | 0.765 | |
| 1h7w | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.764 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.761 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.760 | |
| 4dsg | FAD | Uncharacterized protein | / | 0.759 | |
| 4dsh | FDA | Uncharacterized protein | / | 0.757 | |
| 1cjc | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.752 | |
| 4rpg | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.752 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.752 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.751 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.751 | |
| 1v0j | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.747 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.743 | |
| 1wam | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.742 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.742 | |
| 2jb1 | FAD | L-amino acid oxidase | / | 0.740 | |
| 5l3d | FAD | Lysine-specific histone demethylase 1A | 1 | 0.737 | |
| 2jb2 | FAD | L-amino acid oxidase | / | 0.736 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.736 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.736 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.735 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.730 | |
| 4u8o | FDA | UDP-galactopyranose mutase | / | 0.730 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.728 | |
| 1ps9 | FAD | 2,4-dienoyl-CoA reductase | 1.3.1.34 | 0.727 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.727 | |
| 3int | FDA | UDP-galactopyranose mutase | 5.4.99.9 | 0.727 | |
| 4o5u | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.726 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.725 | |
| 3qj4 | FAD | Renalase | / | 0.723 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.722 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.720 | |
| 2bab | FAD | Putative aminooxidase | / | 0.719 | |
| 1gte | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.718 | |
| 4u8n | FDA | UDP-galactopyranose mutase | / | 0.718 | |
| 4wx1 | FDA | UDP-galactopyranose mutase | / | 0.718 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.717 | |
| 4i58 | FAD | Cyclohexylamine Oxidase | / | 0.717 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.716 | |
| 4u8m | FDA | UDP-galactopyranose mutase | / | 0.716 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.715 | |
| 3utg | FDA | UDP-galactopyranose mutase | / | 0.715 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.715 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.714 | |
| 4rph | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.714 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.713 | |
| 2bac | FAD | Putative aminooxidase | / | 0.712 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.712 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.710 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.710 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.709 | |
| 2bi8 | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.708 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.708 | |
| 3uth | FDA | UDP-galactopyranose mutase | / | 0.708 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.708 | |
| 4u8i | FDA | UDP-galactopyranose mutase | / | 0.708 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.707 | |
| 1f8r | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.706 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.706 | |
| 4o5q | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.706 | |
| 1e1m | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.704 | |
| 2gqf | FAD | Uncharacterized protein HI_0933 | / | 0.704 | |
| 1e1l | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.703 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.703 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.702 | |
| 4u8k | FDA | UDP-galactopyranose mutase | / | 0.702 | |
| 1lqu | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.701 | |
| 4ykg | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.701 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.700 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.699 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.698 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.697 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.695 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.694 | |
| 3lzx | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.694 | |
| 1cc2 | FAD | Cholesterol oxidase | 1.1.3.6 | 0.692 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.692 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.692 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.692 | |
| 3rha | FDA | Putrescine oxidase | / | 0.692 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.692 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.691 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.691 | |
| 3cgd | FAD | Coenzyme A disulfide reductase | / | 0.691 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.691 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.691 | |
| 4u8l | FDA | UDP-galactopyranose mutase | / | 0.691 | |
| 4ykf | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.691 | |
| 4h4p | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.690 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.689 | |
| 1yy5 | FAD | Polyamine oxidase FMS1 | / | 0.689 | |
| 3ef6 | FAD | Toluene 1,2-dioxygenase system ferredoxin--NAD(+) reductase component | 1.18.1.3 | 0.689 | |
| 3ict | FAD | Coenzyme A disulfide reductase | / | 0.689 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.688 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.688 | |
| 1f3p | FAD | Ferredoxin reductase | / | 0.688 | |
| 3kve | FAD | L-amino-acid oxidase | / | 0.687 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.686 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.686 | |
| 3cgc | FAD | Coenzyme A disulfide reductase | / | 0.686 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.686 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.686 | |
| 1i8t | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.685 | |
| 1gaw | FAD | Ferredoxin | / | 0.684 | |
| 2c7g | FAD | NADPH-ferredoxin reductase FprA | 1.18.1.2 | 0.684 | |
| 2cvj | FAD | Thioredoxin reductase related protein | / | 0.684 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.684 | |
| 4rpj | FAD | UDP-galactopyranose mutase | 5.4.99.9 | 0.683 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.682 | |
| 3ukl | FAD | UDP-galactopyranose mutase | / | 0.681 | |
| 1mo9 | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.680 | |
| 2ywl | FAD | Thioredoxin reductase related protein | / | 0.680 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.680 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.680 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.680 | |
| 4u8j | FDA | UDP-galactopyranose mutase | / | 0.679 | |
| 5fs9 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.679 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.678 | |
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 0.678 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.678 | |
| 4u2l | SFD | Cholesterol oxidase | 1.1.3.6 | 0.678 | |
| 1get | FAD | Glutathione reductase | 1.8.1.7 | 0.677 | |
| 2gr0 | FAD | Ferredoxin reductase | / | 0.677 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.677 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.677 | |
| 3kkj | FAD | Renalase | / | 0.677 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.677 | |
| 4kpr | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.677 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.676 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.676 | |
| 4opg | FDA | Conserved Archaeal protein | / | 0.676 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.675 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.675 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.675 | |
| 3cge | FAD | Coenzyme A disulfide reductase | / | 0.675 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.674 | |
| 4u8p | FDA | UDP-galactopyranose mutase | / | 0.674 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.674 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.673 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.673 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.673 | |
| 4opt | FDA | Conserved Archaeal protein | / | 0.673 | |
| 1bx0 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.672 | |
| 2x8h | FAD | Thioredoxin glutathione reductase | / | 0.672 | |
| 3utf | FDA | UDP-galactopyranose mutase | / | 0.672 | |
| 4qi4 | FAD | Cellobiose dehydrogenase | / | 0.672 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.671 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 0.671 | |
| 3fbs | FAD | Oxidoreductase | / | 0.671 | |
| 3oc4 | FAD | Oxidoreductase, pyridine nucleotide-disulfide family | / | 0.671 | |
| 4fk1 | FAD | Putative thioredoxin reductase | / | 0.671 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.670 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.669 | |
| 1e1k | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.669 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.669 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.669 | |
| 3dgz | FAD | Thioredoxin reductase 2, mitochondrial | 1.8.1.9 | 0.669 | |
| 3qvr | FAD | Glucose oxidase | 1.1.3.4 | 0.669 | |
| 4j33 | FAD | Kynurenine 3-monooxygenase | / | 0.669 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.669 | |
| 2c3d | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.668 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.667 | |
| 1jnr | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.666 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.665 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.665 | |
| 2q0k | FAD | Thioredoxin reductase | 1.8.1.9 | 0.665 | |
| 2ylw | FAD | Phenylacetone monooxygenase | 1.14.13.92 | 0.665 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.665 | |
| 3ics | FAD | Coenzyme A disulfide reductase | / | 0.665 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.665 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.664 | |
| 4a65 | FAD | Thioredoxin reductase | / | 0.664 | |
| 4opi | FDA | Conserved Archaeal protein | / | 0.664 | |
| 4u2s | FDA | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 2cul | FAD | GidA-related protein | / | 0.663 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.663 | |
| 3ad9 | NAD | Subunit alpha of sarocosine oxidase | / | 0.663 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3lad | FAD | Dihydrolipoyl dehydrogenase | / | 0.663 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.663 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.662 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.662 | |
| 4lii | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.662 | |
| 3dgh | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.661 | |
| 3atr | FDA | Conserved Archaeal protein | / | 0.660 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.660 | |
| 1cbo | FAD | Cholesterol oxidase | 1.1.3.6 | 0.659 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.659 | |
| 4h4z | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.659 | |
| 4hmw | FMN | Pyridoxamine 5'-phosphate oxidase | / | 0.659 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.659 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.658 | |
| 4z26 | FAD | Putative GMC-type oxidoreductase R135 | 1 | 0.658 | |
| 1nhp | FAD | NADH peroxidase | 1.11.1.1 | 0.657 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.657 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.657 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.657 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.657 | |
| 1fnd | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.656 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.656 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.656 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.656 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.656 | |
| 1gaq | FAD | Ferredoxin | / | 0.655 | |
| 1sez | FAD | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.655 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.655 | |
| 2h94 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.654 | |
| 2wow | FAD | Trypanothione reductase | / | 0.654 | |
| 4b68 | FAD | L-ornithine N(5)-monooxygenase | / | 0.654 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.654 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 1tdo | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.653 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.653 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.653 | |
| 2gh5 | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.652 | |
| 1tdk | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.651 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.651 | |
| 2fjd | SFD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.651 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.651 | |
| 4em3 | FAD | Coenzyme A disulfide reductase | / | 0.651 | |
| 1gv4 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.650 | |
| 1nhr | FAD | NADH peroxidase | 1.11.1.1 | 0.650 | |
| 1tdn | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.650 | |
| 4j56 | FAD | Thioredoxin reductase 2 | 1.8.1.9 | 0.650 | |
| 4jdr | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.650 | |
| 4nte | FAD | DepH | / | 0.650 |