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 |
|---|---|---|---|
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1knp | FAD | L-aspartate oxidase | 1.4.3.16 | 1.488 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 1.264 | |
| 5c3j | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.051 | |
| 5c2t | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 1.022 | |
| 4ytn | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.945 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.922 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.911 | |
| 3aeb | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.885 | |
| 1qo8 | FAD | Fumarate reductase flavoprotein subunit | / | 0.874 | |
| 4kx6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.835 | |
| 1d4c | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.822 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.816 | |
| 4yxd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.801 | |
| 3cuk | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.789 | |
| 4wct | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.770 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.769 | |
| 5ez7 | FAD | Probable FAD-dependent oxidoreductase PA4991 | / | 0.768 | |
| 2i0z | FAD | NAD(FAD)-utilizing dehydrogenases | / | 0.766 | |
| 1ng3 | FAD | Glycine oxidase | 1.4.3.19 | 0.765 | |
| 3pvc | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.761 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.751 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.749 | |
| 1c0l | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.744 | |
| 3gsi | FAD | Dimethylglycine oxidase | 1.5.3.10 | 0.743 | |
| 1kf6 | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.742 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.742 | |
| 4cnk | FAD | L-amino acid oxidase | / | 0.740 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.739 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.738 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.735 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.731 | |
| 4nte | FAD | DepH | / | 0.729 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.721 | |
| 3ae4 | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.721 | |
| 4yjd | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.720 | |
| 1ng4 | FAD | Glycine oxidase | 1.4.3.19 | 0.719 | |
| 3lsi | FAD | Pyranose 2-oxidase | / | 0.717 | |
| 3fbs | FAD | Oxidoreductase | / | 0.716 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.716 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.716 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.715 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.714 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.713 | |
| 1d4d | FAD | Fumarate reductase flavoprotein subunit | 1.3.5.4 | 0.712 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.711 | |
| 4cnj | FAD | L-amino acid oxidase | / | 0.710 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.709 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.708 | |
| 4o5q | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.708 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.707 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.707 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.707 | |
| 4jn9 | FAD | DepH | / | 0.705 | |
| 4opu | FDA | Conserved Archaeal protein | / | 0.705 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.704 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.701 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.697 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.697 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.696 | |
| 3oz2 | FAD | Digeranylgeranylglycerophospholipid reductase | / | 0.696 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.696 | |
| 2qcu | FAD | Aerobic glycerol-3-phosphate dehydrogenase | 1.1.5.3 | 0.695 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.694 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.694 | |
| 4ynt | FDA | Glucose oxidase, putative | / | 0.694 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.693 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.692 | |
| 4up3 | FAD | Thioredoxin reductase | / | 0.692 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.691 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.688 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.687 | |
| 2yg6 | FAD | Putrescine oxidase | / | 0.687 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.687 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.687 | |
| 4ysh | FAD | Glycine oxidase | / | 0.687 | |
| 4o5u | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.686 | |
| 4ntc | FAD | Thioredoxin reductase gliT | / | 0.685 | |
| 4nev | FAD | Trypanothione reductase | / | 0.684 | |
| 4uir | FAD | Oleate hydratase | 4.2.1.53 | 0.684 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.683 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.682 | |
| 3lzw | FAD | Ferredoxin--NADP reductase 2 | 1.18.1.2 | 0.682 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.682 | |
| 3r9u | FAD | Thioredoxin reductase | / | 0.681 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.680 | |
| 1rz1 | FAD | Phenol 2-hydroxylase component B | / | 0.679 | |
| 2y48 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.679 | |
| 2zzc | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.678 | |
| 3sgl | FAD | tRNA 5-methylaminomethyl-2-thiouridine biosynthesis bifunctional protein MnmC | / | 0.678 | |
| 3fcj | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.677 | |
| 3uox | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.677 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.676 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.676 | |
| 3f8d | FAD | NADH oxidase/thioredoxin reductase | / | 0.676 | |
| 5hxw | FAD | L-amino acid deaminase | / | 0.676 | |
| 2reh | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.675 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.675 | |
| 2bac | FAD | Putative aminooxidase | / | 0.673 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.673 | |
| 3icr | FAD | Coenzyme A disulfide reductase | / | 0.673 | |
| 2fje | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.672 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.672 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.671 | |
| 4opd | FDA | Conserved Archaeal protein | / | 0.671 | |
| 1cf3 | FAD | Glucose oxidase | 1.1.3.4 | 0.670 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.670 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.670 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.669 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.668 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.668 | |
| 2rgo | FAD | Alpha-Glycerophosphate Oxidase | / | 0.668 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.668 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.668 | |
| 1gpe | FAD | Glucose oxidase | 1.1.3.4 | 0.667 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.667 | |
| 1vrq | FMN | Subunit alpha of sarocosine oxidase | / | 0.666 | |
| 1vrq | FMN | Subunit beta of sarcosine oxidase | / | 0.666 | |
| 2hfo | FMN | Activator of photopigment and puc expression | / | 0.666 | |
| 4opc | FDA | Conserved Archaeal protein | / | 0.666 | |
| 2zbw | FAD | Ferredoxin--NADP reductase | / | 0.665 | |
| 3k4c | FAD | Pyranose 2-oxidase | / | 0.664 | |
| 4nwz | FAD | FAD-dependent pyridine nucleotide-disulfide oxidoreductase | / | 0.664 | |
| 1fea | FAD | Trypanothione reductase | 1.8.1.12 | 0.663 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.663 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.663 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.663 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.663 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.663 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.663 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.662 | |
| 1sez | FAD | Protoporphyrinogen oxidase, mitochondrial | 1.3.3.4 | 0.662 | |
| 2bab | FAD | Putative aminooxidase | / | 0.662 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.662 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.662 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.661 | |
| 2b9w | FAD | Putative aminooxidase | / | 0.661 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.661 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.661 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.660 | |
| 4h4t | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.659 | |
| 4p13 | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.659 | |
| 1vdc | FAD | Thioredoxin reductase 1, mitochondrial | 1.8.1.9 | 0.658 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.658 | |
| 2tpr | FAD | Trypanothione reductase | 1.8.1.12 | 0.658 | |
| 3pfd | FDA | Acyl-CoA dehydrogenase FadE25 | / | 0.658 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.658 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.658 | |
| 2byc | FMN | Blue-light receptor of the BLUF-family | / | 0.657 | |
| 2f5z | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.657 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.657 | |
| 3uoz | FAD | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.657 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.657 | |
| 1e1n | FAD | NADPH:adrenodoxin oxidoreductase, mitochondrial | 1.18.1.6 | 0.656 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.656 | |
| 4b1b | FAD | Thioredoxin reductase | 1.8.1.9 | 0.656 | |
| 4hh0 | FMN | AppA protein | / | 0.656 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.655 | |
| 2jk6 | FAD | Trypanothione reductase | / | 0.655 | |
| 2yr5 | FAD | Phenylalanine 2-monooxygenase precursor | 1.13.12.9 | 0.655 | |
| 3qvp | FAD | Glucose oxidase | 1.1.3.4 | 0.655 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.654 | |
| 2yvj | FAD | Ferredoxin reductase | / | 0.654 | |
| 3kkj | FAD | Renalase | / | 0.654 | |
| 3klj | FAD | NADH-rubredoxin oxidoreductase | 1.18.1.1 | 0.654 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.653 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.653 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.652 | |
| 3m0o | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.652 | |
| 3pft | FMN | Flavin reductase | / | 0.652 | |
| 4jq9 | FAD | Dihydrolipoyl dehydrogenase | / | 0.652 | |
| 4x9m | FAD | Uncharacterized protein MG039 homolog | / | 0.652 | |
| 2gr3 | FAD | Ferredoxin reductase | / | 0.651 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.651 | |
| 4x9n | FAD | Uncharacterized protein MG039 homolog | / | 0.651 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.650 |