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 |
|---|---|---|---|
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.357 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.347 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.329 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.315 | |
| 1gr1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.298 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.292 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.290 | |
| 1b2r | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.268 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.266 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.265 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.265 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.264 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.259 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.257 | |
| 1qgz | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.235 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.224 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.207 | |
| 1gaw | FAD | Ferredoxin | / | 1.205 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.204 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.202 | |
| 1bx0 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.199 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.190 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.190 | |
| 1fnd | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.185 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.184 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.182 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.180 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.167 | |
| 1w35 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.159 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.137 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 1.135 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.131 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 1.131 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 1.101 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.087 | |
| 3w5u | FAD | Ferredoxin | / | 1.080 | |
| 1gaq | FAD | Ferredoxin | / | 1.072 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.064 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.050 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 1.025 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 1.012 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.004 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.988 | |
| 2xnc | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.988 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.959 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.956 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.956 | |
| 4yaf | FAD | NADPH--cytochrome P450 reductase | / | 0.956 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.944 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.941 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.938 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.936 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.929 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.926 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 0.924 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.918 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.912 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.905 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.893 | |
| 4yau | FAD | NADPH--cytochrome P450 reductase | / | 0.891 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.886 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.869 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.867 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.865 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.861 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.852 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.837 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.836 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.832 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.828 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.825 | |
| 3ojx | FAD | NADPH--cytochrome P450 reductase | / | 0.802 | |
| 4yao | FAD | NADPH--cytochrome P450 reductase | / | 0.795 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.793 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.791 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.790 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.782 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.775 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.774 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.765 | |
| 1ep3 | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | / | 0.755 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.750 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.742 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.729 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.724 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.724 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.723 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.720 | |
| 4k1x | FAD | NADPH:ferredoxin reductase | / | 0.715 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.712 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.708 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.708 | |
| 3q9t | FAY | Uncharacterized protein | / | 0.706 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.702 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.701 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.700 | |
| 2iml | FMN | Uncharacterized protein | / | 0.697 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.697 | |
| 3hjk | FAD | Vivid PAS protein VVD | / | 0.693 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.689 | |
| 3a20 | FMN | FMN-binding protein | / | 0.680 | |
| 3a6q | FMN | FMN-binding protein | / | 0.680 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.678 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.677 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.677 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.677 | |
| 2igo | FAD | Pyranose 2-oxidase | / | 0.676 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.675 | |
| 5g3s | FDA | Flavin-dependent L-tryptophan oxidase VioA | / | 0.673 | |
| 3lsh | FAD | Pyranose 2-oxidase | / | 0.672 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.672 | |
| 4z2t | FAD | 2-hydroxybiphenyl-3-monooxygenase | / | 0.672 | |
| 3pft | FMN | Flavin reductase | / | 0.671 | |
| 2dji | FAD | Pyruvate oxidase | / | 0.670 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.669 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.668 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.667 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.667 | |
| 1eje | FMN | Protein MTH_152 | / | 0.664 | |
| 2e83 | FMN | FMN-binding protein | / | 0.664 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.664 | |
| 1wli | FMN | FMN-binding protein | / | 0.663 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.663 | |
| 4gus | FAD | Lysine-specific histone demethylase 1B | 1 | 0.663 | |
| 2gv8 | FAD | Thiol-specific monooxygenase | 1.14.13 | 0.661 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.659 | |
| 3a6r | FMN | FMN-binding protein | / | 0.659 | |
| 4eet | FMN | Phototropin-2 | 2.7.11.1 | 0.659 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.658 | |
| 4ees | FMN | Phototropin-2 | 2.7.11.1 | 0.658 | |
| 1v5e | FAD | Pyruvate oxidase | / | 0.656 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.656 | |
| 5cho | FAD | Flavin reductase | / | 0.656 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.655 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.654 | |
| 1usc | FMN | Monooxygenase | / | 0.654 | |
| 1wlk | FMN | FMN-binding protein | / | 0.654 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.653 | |
| 3t37 | FAD | Pyridoxine 4-oxidase | / | 0.652 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.652 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.651 | |
| 4ybn | FAD | Flavin-nucleotide-binding protein | / | 0.651 |