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 |
|---|---|---|---|
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.330 | |
| 1fnb | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.296 | |
| 1fnd | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.260 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.250 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.248 | |
| 1gaw | FAD | Ferredoxin | / | 1.242 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.233 | |
| 1bx0 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 1.229 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.228 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.222 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.209 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 1.197 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.188 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.186 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.180 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.172 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.171 | |
| 1gr1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.169 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.166 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.159 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.159 | |
| 2b5o | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.159 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.159 | |
| 1w35 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.153 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.147 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.145 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.145 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.143 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.133 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.117 | |
| 1w34 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.113 | |
| 3w5u | FAD | Ferredoxin | / | 1.102 | |
| 1qgz | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.091 | |
| 1b2r | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 1.083 | |
| 1gaq | FAD | Ferredoxin | / | 1.082 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 1.075 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 1.073 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 1.035 | |
| 4af7 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.023 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 1.016 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 1.010 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 1.009 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.976 | |
| 1ewy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.974 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.964 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.959 | |
| 4yau | FAD | NADPH--cytochrome P450 reductase | / | 0.946 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.943 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.932 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.931 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.914 | |
| 1f20 | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.905 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.905 | |
| 2xnc | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.904 | |
| 3w5h | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.904 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.900 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.896 | |
| 1tll | FAD | Nitric oxide synthase, brain | 1.14.13.39 | 0.895 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.891 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.890 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.888 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.884 | |
| 4yaf | FAD | NADPH--cytochrome P450 reductase | / | 0.870 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.860 | |
| 3ojx | FAD | NADPH--cytochrome P450 reductase | / | 0.854 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.853 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.845 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.840 | |
| 4yao | FAD | NADPH--cytochrome P450 reductase | / | 0.830 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.825 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.822 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.816 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.815 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.815 | |
| 2eix | FAD | NADH-cytochrome b5 reductase | / | 0.782 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.780 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.775 | |
| 2gpj | FAD | Siderophore-interacting protein | / | 0.770 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.762 | |
| 1ep3 | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | / | 0.761 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.757 | |
| 1cqx | FAD | Flavohemoprotein | / | 0.749 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.747 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.747 | |
| 1krh | FAD | Benzoate 1,2-dioxygenase electron transfer component | 1.18.1.3 | 0.746 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.702 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.702 | |
| 4k1x | FAD | NADPH:ferredoxin reductase | / | 0.700 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.695 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.692 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.690 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.689 | |
| 3vqr | FAD | Putative oxidoreductase | / | 0.687 | |
| 2bgi | FAD | NADPH:ferredoxin reductase | / | 0.686 | |
| 5j60 | FAD | Thioredoxin reductase | / | 0.684 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.680 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.680 | |
| 3pl8 | FAD | Pyranose 2-oxidase | / | 0.679 | |
| 3a3b | RBF | Lumazine protein | / | 0.677 | |
| 3pft | FMN | Flavin reductase | / | 0.677 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.677 | |
| 4l82 | FMN | Uncharacterized protein | / | 0.676 | |
| 4opl | FDA | Conserved Archaeal protein | / | 0.676 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.675 | |
| 1c0k | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.674 | |
| 1eje | FMN | Protein MTH_152 | / | 0.674 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.673 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.673 | |
| 3lsm | SFD | Pyranose 2-oxidase | / | 0.672 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.672 | |
| 3hdy | FDA | UDP-galactopyranose mutase | / | 0.671 | |
| 4mih | FAD | Pyranose 2-oxidase | 1.1.3.10 | 0.671 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.670 | |
| 2aqj | FAD | Flavin-dependent tryptophan halogenase PrnA | 1.14.19.9 | 0.670 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.669 | |
| 3if9 | FAD | Glycine oxidase | 1.4.3.19 | 0.669 | |
| 3v76 | FDA | Uncharacterized protein | / | 0.669 | |
| 1rz1 | FAD | Phenol 2-hydroxylase component B | / | 0.668 | |
| 1wlk | FMN | FMN-binding protein | / | 0.668 | |
| 3lov | FAD | Protoporphyrinogen oxidase | / | 0.668 | |
| 2b9y | FAD | Putative aminooxidase | / | 0.667 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.667 | |
| 3mkh | FAD | Nitroalkane oxidase | / | 0.667 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.667 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.666 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.664 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.664 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.663 | |
| 1gth | FAD | Dihydropyrimidine dehydrogenase [NADP(+)] | 1.3.1.2 | 0.662 | |
| 1pkv | RBF | Riboflavin synthase | 2.5.1.9 | 0.662 | |
| 3ge6 | FMN | Nitroreductase | / | 0.662 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.662 | |
| 1rz0 | FAD | Phenol 2-hydroxylase component B | / | 0.660 | |
| 2nr4 | FMN | Conserved protein | / | 0.660 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.660 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.659 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.659 | |
| 3ukf | FDA | UDP-galactopyranose mutase | / | 0.658 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.658 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.657 | |
| 4hia | FMN | LOV protein | / | 0.657 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.656 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.656 | |
| 4fwf | FAD | Lysine-specific histone demethylase 1B | 1 | 0.656 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.656 | |
| 3axb | FAD | Putative oxidoreductase | / | 0.655 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.655 | |
| 4qvb | F42 | F420H(2)-dependent reductase Rv1155 | 1.4.3.5 | 0.655 | |
| 5djt | FMN | NPH1-2 | / | 0.654 | |
| 1h81 | FAD | Polyamine oxidase | 1.5.3.14 | 0.653 | |
| 2du8 | FAD | D-amino-acid oxidase | 1.4.3.3 | 0.653 | |
| 4gde | FDA | UDP-galactopyranose mutase | / | 0.653 | |
| 2q9u | FMN | A-type flavoprotein | / | 0.652 | |
| 3kpf | FAD | Polyamine oxidase | 1.5.3.14 | 0.652 | |
| 4z2t | FAD | 2-hydroxybiphenyl-3-monooxygenase | / | 0.651 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.650 |