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 |
|---|---|---|---|
| 3d72 | FAD | Vivid PAS protein VVD |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3d72 | FAD | Vivid PAS protein VVD | / | 1.523 | |
| 3is2 | FAD | Vivid PAS protein VVD | / | 1.399 | |
| 3hji | FAD | Vivid PAS protein VVD | / | 1.388 | |
| 2pd8 | FAD | Vivid PAS protein VVD | / | 1.384 | |
| 2pd7 | FAD | Vivid PAS protein VVD | / | 1.336 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 1.315 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 1.166 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 1.030 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 1.022 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 1.010 | |
| 4eep | FMN | Phototropin-2 | 2.7.11.1 | 0.999 | |
| 4eeu | FMN | Phototropin-2 | 2.7.11.1 | 0.994 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.990 | |
| 5djt | FMN | NPH1-2 | / | 0.971 | |
| 1n9l | FMN | Putative blue light receptor | / | 0.969 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.961 | |
| 4hia | FMN | LOV protein | / | 0.951 | |
| 1n9n | FMN | Putative blue light receptor | / | 0.950 | |
| 5efw | FMN | NPH1-1 | / | 0.942 | |
| 5dju | FMN | NPH1-2 | / | 0.940 | |
| 4hj3 | FMN | LOV protein | / | 0.934 | |
| 4r38 | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.934 | |
| 2v1a | FMN | NPH1-1 | / | 0.931 | |
| 2v0u | FMN | NPH1-1 | / | 0.929 | |
| 4hj6 | FMN | LOV protein | / | 0.904 | |
| 5j3w | FMN | Sensory box protein | / | 0.895 | |
| 4kuo | RBF | Putative blue-light photoreceptor | / | 0.887 | |
| 4eer | FMN | Phototropin-2 | 2.7.11.1 | 0.886 | |
| 4wf0 | FMN | NPH1-1 | / | 0.886 | |
| 1g28 | FMN | PHY3 | / | 0.879 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.862 | |
| 5j4e | FMN | Sensory box protein | / | 0.849 | |
| 4hnb | FMN | LOV protein | / | 0.846 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.842 | |
| 3t50 | FMN | Blue-light-activated histidine kinase | 2.7.13.3 | 0.833 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.807 | |
| 4hj4 | FMN | LOV protein | / | 0.786 | |
| 3p7n | FMN | Light-activated DNA-binding protein EL222 | / | 0.779 | |
| 3ue6 | FMN | Aureochrome1 | / | 0.772 | |
| 4r3a | RBF | Blue-light-activated histidine kinase 2 | 2.7.13.3 | 0.765 | |
| 3sw1 | FMN | Sensory box protein | / | 0.761 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.735 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.731 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.729 | |
| 3mzi | FMN | Activator of photopigment and puc expression | / | 0.726 | |
| 2iid | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.724 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.713 | |
| 1f8s | FAD | L-amino-acid oxidase | 1.4.3.2 | 0.705 | |
| 3nyc | FAD | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.705 | |
| 4yus | FMN | Family 3 adenylate cyclase | / | 0.703 | |
| 1jeh | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.699 | |
| 5dkk | FMN | Predicted protein | / | 0.699 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.698 | |
| 5cho | FAD | Flavin reductase | / | 0.698 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.696 | |
| 1tj1 | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.695 | |
| 3ad9 | FAD | Subunit beta of sarcosine oxidase | / | 0.694 | |
| 2hfn | FMN | Activator of photopigment and puc expression | / | 0.692 | |
| 4hh0 | FMN | AppA protein | / | 0.692 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.691 | |
| 4d5g | FAD | Cyclohexane-1,2-dione hydrolase | 3.7.1.11 | 0.690 | |
| 1usc | FMN | Monooxygenase | / | 0.688 | |
| 2yqu | FAD | Dihydrolipoyl dehydrogenase | / | 0.687 | |
| 1fl2 | FAD | Alkyl hydroperoxide reductase subunit F | 1.8.1 | 0.686 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.686 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.685 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.685 | |
| 3ic9 | FAD | Putative dihydrolipoamide dehydrogenase | / | 0.685 | |
| 2fzn | FAD | Bifunctional protein PutA | 1.5.5.2 | 0.684 | |
| 2q7v | FAD | Thioredoxin reductase | / | 0.684 | |
| 1ve9 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.682 | |
| 3nlc | FAD | Uncharacterized protein | / | 0.682 | |
| 3urh | FAD | Dihydrolipoyl dehydrogenase | / | 0.681 | |
| 1n07 | FMN | Riboflavin kinase | 2.7.1.26 | 0.680 | |
| 3cls | FAD | Electron transfer flavoprotein subunit alpha | / | 0.677 | |
| 1trb | FAD | Thioredoxin reductase | 1.8.1.9 | 0.674 | |
| 2zaf | FAD | Nitroalkane oxidase | 1.7.3.1 | 0.673 | |
| 5br7 | FAD | UDP-galactopyranose mutase | / | 0.673 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.671 | |
| 1b4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 1j8q | FMN | Flavodoxin | / | 0.670 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.670 | |
| 1v59 | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.669 | |
| 4j2w | FAD | Kynurenine 3-monooxygenase | / | 0.669 | |
| 4q72 | FAD | Bifunctional protein PutA | / | 0.669 | |
| 1ebd | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.668 | |
| 1joa | FAD | NADH peroxidase | 1.11.1.1 | 0.668 | |
| 4qi7 | FAD | Cellobiose dehydrogenase | / | 0.668 | |
| 4udq | FAD | 5-(hydroxymethyl)furfural oxidase | / | 0.668 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.668 | |
| 1cl0 | FAD | Thioredoxin reductase | 1.8.1.9 | 0.667 | |
| 1zmc | FAD | Dihydrolipoyl dehydrogenase, mitochondrial | 1.8.1.4 | 0.667 | |
| 3all | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.667 | |
| 1tdf | FAD | Thioredoxin reductase | 1.8.1.9 | 0.666 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.666 | |
| 2bac | FAD | Putative aminooxidase | / | 0.666 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.666 | |
| 3gmb | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.666 | |
| 1kif | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.665 | |
| 1nb9 | RBF | Riboflavin kinase | 2.7.1.26 | 0.665 | |
| 2whd | FAD | Thioredoxin reductase | / | 0.665 | |
| 4e2b | FMN | Dehydrogenase | / | 0.665 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.665 | |
| 4j36 | FAD | Kynurenine 3-monooxygenase | / | 0.665 | |
| 2v18 | FMN | Dodecin | / | 0.664 | |
| 4bk3 | FAD | Probable salicylate monooxygenase | / | 0.663 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.662 | |
| 3sfe | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.661 | |
| 4h2p | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.661 | |
| 2b9x | FAD | Putative aminooxidase | / | 0.660 | |
| 2eq7 | FAD | Dihydrolipoyl dehydrogenase | / | 0.660 | |
| 3ept | FDA | Putative FAD-monooxygenase | / | 0.660 | |
| 3ish | FAD | Thioredoxin reductase | 1.8.1.9 | 0.660 | |
| 4a5l | FAD | Thioredoxin reductase | / | 0.660 | |
| 4mok | FAD | Pyranose 2-oxidase | / | 0.660 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.659 | |
| 4rsl | FAD | Fructosyl peptide oxidase | / | 0.659 | |
| 5buk | FAD | FADH2-dependent halogenase | / | 0.659 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.658 | |
| 3a3g | DLZ | Lumazine protein | / | 0.658 | |
| 4ccq | FAD | Thioredoxin reductase | / | 0.658 | |
| 1tde | FAD | Thioredoxin reductase | 1.8.1.9 | 0.656 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.656 | |
| 3a3b | RBF | Lumazine protein | / | 0.656 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.656 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.655 | |
| 2gmh | FAD | Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrial | 1.5.5.1 | 0.655 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.654 | |
| 2bab | FAD | Putative aminooxidase | / | 0.654 | |
| 3qfa | FAD | Thioredoxin reductase 1, cytoplasmic | 1.8.1.9 | 0.653 | |
| 3sfd | FAD | Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial | / | 0.653 | |
| 5i39 | FAD | L-amino acid deaminase | / | 0.653 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.652 | |
| 1ryi | FAD | Glycine oxidase | 1.4.3.19 | 0.652 | |
| 4irn | FAD | AnaB | / | 0.652 | |
| 5g3t | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.652 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.651 | |
| 3f90 | FMN | Flavodoxin | / | 0.651 | |
| 4jy2 | FAD | 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase | / | 0.651 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.651 | |
| 1s4m | LUM | Riboflavin biosynthesis protein | / | 0.650 | |
| 2a8x | FAD | Dihydrolipoyl dehydrogenase | 1.8.1.4 | 0.650 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.650 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.650 | |
| 4i6g | FAD | Cryptochrome-2 | / | 0.650 | |
| 4rek | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.650 |