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 |
|---|---|---|---|
| 3e4v | FMN | Uncharacterized protein |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 3e4v | FMN | Uncharacterized protein | / | 1.422 | |
| 1i0s | FMN | Ferric-chelate reductase (NAD(P)H) | / | 0.931 | |
| 1usc | FMN | Monooxygenase | / | 0.892 | |
| 3bnk | FMN | Flavoredoxin | / | 0.867 | |
| 5cho | FAD | Flavin reductase | / | 0.774 | |
| 2pia | FMN | Phthalate dioxygenase reductase | / | 0.772 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.761 | |
| 4f07 | FAD | Styrene monooxygenase component 2 | / | 0.757 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.756 | |
| 3jqr | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.754 | |
| 2rc5 | FAD | Ferredoxin--NADP reductase | / | 0.745 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.745 | |
| 4fk8 | FAD | Ferredoxin--NADP reductase | / | 0.744 | |
| 3qe2 | FAD | NADPH--cytochrome P450 reductase | / | 0.743 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.742 | |
| 3qfc | FAD | NADPH--cytochrome P450 reductase | / | 0.742 | |
| 3ge6 | FMN | Nitroreductase | / | 0.740 | |
| 1bx1 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.738 | |
| 3qfr | FAD | NADPH--cytochrome P450 reductase | / | 0.737 | |
| 4hms | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.735 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.732 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.732 | |
| 2ok8 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.729 | |
| 1gvh | FAD | Flavohemoprotein | / | 0.727 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.726 | |
| 1ty9 | FMN | Phenazine biosynthesis protein PhzG | 1.4 | 0.723 | |
| 3vy2 | FMN | FMN-binding protein | / | 0.723 | |
| 1amo | FAD | NADPH--cytochrome P450 reductase | / | 0.721 | |
| 2ptf | FMN | Uncharacterized protein MTH_863 | / | 0.721 | |
| 1eje | FMN | Protein MTH_152 | / | 0.720 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.720 | |
| 3cox | FAD | Cholesterol oxidase | 1.1.3.6 | 0.720 | |
| 2bf4 | FAD | NADPH--cytochrome P450 reductase | / | 0.719 | |
| 2bpo | FAD | NADPH--cytochrome P450 reductase | / | 0.719 | |
| 2bn4 | FAD | NADPH--cytochrome P450 reductase | / | 0.718 | |
| 1ogi | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.716 | |
| 3qfs | FAD | NADPH--cytochrome P450 reductase | / | 0.713 | |
| 3qft | FAD | NADPH--cytochrome P450 reductase | / | 0.712 | |
| 2ou5 | FMN | Pyridoxamine 5'-phosphate oxidase-related FMN-binding protein | / | 0.711 | |
| 2bgj | FAD | NADPH:ferredoxin reductase | / | 0.710 | |
| 3a6q | FMN | FMN-binding protein | / | 0.710 | |
| 4b4d | FAD | Ferredoxin-NADP reductase | / | 0.710 | |
| 2pr5 | FMN | Blue-light photoreceptor | / | 0.709 | |
| 3fpk | FAD | Ferredoxin-NADP reductase | / | 0.708 | |
| 4uaj | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.708 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.708 | |
| 1gaq | FAD | Ferredoxin | / | 0.707 | |
| 2z6c | FMN | Phototropin-1 | 2.7.11.1 | 0.707 | |
| 4y9u | FAD | NADPH--cytochrome P450 reductase | / | 0.707 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.706 | |
| 1gr1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.704 | |
| 4hmx | FMN | Pyridoxamine 5'-phosphate oxidase | / | 0.704 | |
| 1go2 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.703 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.703 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.702 | |
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 0.702 | |
| 3w2e | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.702 | |
| 2qdx | FAD | Ferredoxin--NADP+ reductase | / | 0.701 | |
| 2xnc | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.701 | |
| 3ojw | FAD | NADPH--cytochrome P450 reductase | / | 0.701 | |
| 1e63 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.700 | |
| 1ylr | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.700 | |
| 1mok | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.699 | |
| 3a3b | RBF | Lumazine protein | / | 0.698 | |
| 4y7c | FAD | NADPH--cytochrome P450 reductase | / | 0.698 | |
| 1gjr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.696 | |
| 1qg0 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.696 | |
| 3a6r | FMN | FMN-binding protein | / | 0.696 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.696 | |
| 1wli | FMN | FMN-binding protein | / | 0.695 | |
| 1e62 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.694 | |
| 1fue | FMN | Flavodoxin | / | 0.693 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.692 | |
| 3pft | FMN | Flavin reductase | / | 0.692 | |
| 4hmw | FMN | Pyridoxamine 5'-phosphate oxidase | / | 0.692 | |
| 4kuk | RBF | Putative blue-light photoreceptor | / | 0.692 | |
| 2rc6 | FAD | Ferredoxin--NADP reductase | / | 0.691 | |
| 3rh7 | FMN | Uncharacterized protein | / | 0.691 | |
| 1fdr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.690 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.690 | |
| 2e83 | FMN | FMN-binding protein | / | 0.689 | |
| 2r6h | FAD | Na(+)-translocating NADH-quinone reductase subunit F | / | 0.689 | |
| 3zbt | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.689 | |
| 4xoo | FMN | Coenzyme F420:L-glutamate ligase | / | 0.689 | |
| 4ylf | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog | / | 0.689 | |
| 1n4w | FAD | Cholesterol oxidase | 1.1.3.6 | 0.688 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.688 | |
| 3a20 | FMN | FMN-binding protein | / | 0.688 | |
| 5j3w | FMN | Sensory box protein | / | 0.687 | |
| 3of4 | FMN | Nitroreductase | / | 0.686 | |
| 4n82 | FMN | Ribonucleotide reductase (NrdI family protein), putative | / | 0.686 | |
| 4rhe | FMN | Flavin prenyltransferase UbiX | / | 0.686 | |
| 3fg2 | FAD | Putative rubredoxin reductase | / | 0.684 | |
| 1bjk | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.683 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.683 | |
| 1bx0 | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.682 | |
| 1flm | FMN | FMN-binding protein | / | 0.682 | |
| 2z6d | FMN | Phototropin-2 | 2.7.11.1 | 0.682 | |
| 3w2f | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.682 | |
| 1rz0 | FAD | Phenol 2-hydroxylase component B | / | 0.681 | |
| 4xwr | FAD | Cholesterol oxidase | 1.1.3.6 | 0.681 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.680 | |
| 1ja1 | FAD | NADPH--cytochrome P450 reductase | / | 0.679 | |
| 4xwz | FAD | Fructosyl amine:oxygen oxidoreductase | / | 0.679 | |
| 1h42 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.678 | |
| 3awh | FMN | FMN-binding protein | / | 0.678 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.677 | |
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.675 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.675 | |
| 2vnk | FAD | NADPH:ferredoxin reductase | / | 0.675 | |
| 3n3a | FMN | Protein NrdI | / | 0.675 | |
| 1qgy | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.674 | |
| 2fcr | FMN | Flavodoxin | / | 0.674 | |
| 2ok7 | FAD | Ferredoxin--NADP reductase, apicoplast | / | 0.674 | |
| 3vy5 | FMN | FMN-binding protein | / | 0.674 | |
| 4h4r | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.674 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 0.673 | |
| 3vo2 | FAD | Ferredoxin--NADP reductase | / | 0.673 | |
| 1kqc | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.672 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.671 | |
| 2gqw | FAD | Ferredoxin reductase | / | 0.671 | |
| 3nta | FAD | FAD-dependent pyridine nucleotide-disulphide oxidoreductase | / | 0.671 | |
| 4wuj | FMN | Glycoside hydrolase family 15, cellulose signaling associated protein envoy | / | 0.671 | |
| 1gaw | FAD | Ferredoxin | / | 0.670 | |
| 2vnh | FAD | NADPH:ferredoxin reductase | / | 0.670 | |
| 4bpr | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.670 | |
| 4h4v | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.670 | |
| 4xxg | FAD | Cholesterol oxidase | 1.1.3.6 | 0.670 | |
| 5af7 | FAD | Acyl-CoA dehydrogenase | / | 0.669 | |
| 3bm1 | FMN | Putative NAD(P)H nitroreductase YdjA | / | 0.668 | |
| 4bv6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.668 | |
| 1b8s | FAD | Cholesterol oxidase | 1.1.3.6 | 0.667 | |
| 1wv4 | FMN | Pyridoxine/pyridoxamine 5'-phosphate oxidase | / | 0.667 | |
| 3amf | FMN | FMN-binding protein | / | 0.667 | |
| 3crz | FAD | Ferredoxin--NADP+ reductase | / | 0.667 | |
| 4yau | FAD | NADPH--cytochrome P450 reductase | / | 0.667 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.666 | |
| 1h85 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.666 | |
| 1w87 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.666 | |
| 2w5u | FMN | Flavodoxin | / | 0.666 | |
| 3klb | FMN | Uncharacterized protein | / | 0.666 | |
| 3ukk | FAD | UDP-galactopyranose mutase | / | 0.666 | |
| 4k1x | FAD | NADPH:ferredoxin reductase | / | 0.666 | |
| 4l82 | FMN | Uncharacterized protein | / | 0.666 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.665 | |
| 1sm4 | FAD | Ferredoxin--NADP reductase | / | 0.665 | |
| 3mj4 | FAD | UDP-galactopyranose mutase | / | 0.665 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.665 | |
| 1e64 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.664 | |
| 3f6s | FMN | Flavodoxin | / | 0.664 | |
| 3gyj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.664 | |
| 4af6 | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.664 | |
| 4h4x | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.664 | |
| 4y9r | FAD | NADPH--cytochrome P450 reductase | / | 0.664 | |
| 1b2r | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.663 | |
| 1n4u | FAE | Cholesterol oxidase | 1.1.3.6 | 0.663 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.663 | |
| 2pdt | FAD | Vivid PAS protein VVD | / | 0.663 | |
| 1ci0 | FMN | Pyridoxamine 5'-phosphate oxidase | 1.4.3.5 | 0.662 | |
| 1n1p | FAD | Cholesterol oxidase | 1.1.3.6 | 0.662 | |
| 3a3g | DLZ | Lumazine protein | / | 0.662 | |
| 2iml | FMN | Uncharacterized protein | / | 0.661 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.661 | |
| 4iv6 | FDA | Isovaleryl-CoA dehydrogenase | / | 0.661 | |
| 5er0 | FAD | Uncharacterized NAD(FAD)-dependent dehydrogenase | / | 0.661 | |
| 1c7f | FMN | Flavodoxin | / | 0.660 | |
| 1ooq | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.660 | |
| 3cgb | FAD | Coenzyme A disulfide reductase | / | 0.660 | |
| 3bem | FMN | Putative NAD(P)H nitroreductase MhqN | 1 | 0.659 | |
| 4c43 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.659 | |
| 4fk1 | FAD | Putative thioredoxin reductase | / | 0.659 | |
| 4hj4 | FMN | LOV protein | / | 0.658 | |
| 4lii | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.658 | |
| 1ep3 | FAD | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | / | 0.657 | |
| 1ja0 | FAD | NADPH--cytochrome P450 reductase | / | 0.657 | |
| 2vxa | RBF | Dodecin | / | 0.657 | |
| 3ab1 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.657 | |
| 3gyi | FAD | Cholesterol oxidase | 1.1.3.6 | 0.657 | |
| 4h4p | FAD | Biphenyl dioxygenase ferredoxin reductase subunit | / | 0.657 | |
| 1d7y | FAD | Ferredoxin reductase | / | 0.656 | |
| 2hpv | FMN | FMN-dependent NADH-azoreductase | 1.7 | 0.656 | |
| 3r5w | F42 | Deazaflavin-dependent nitroreductase | / | 0.656 | |
| 2v5v | FMN | Flavodoxin | / | 0.655 | |
| 3mhp | FAD | Ferredoxin--NADP reductase, leaf isozyme, chloroplastic | 1.18.1.2 | 0.655 | |
| 3x21 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.655 | |
| 1fnd | FAD | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.654 | |
| 3cnj | FAD | Cholesterol oxidase | 1.1.3.6 | 0.654 | |
| 3m13 | FAD | Monomeric sarcosine oxidase | 1.5.3.1 | 0.654 | |
| 4bmp | FMN | Protein NrdI | / | 0.654 | |
| 4g73 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.654 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.653 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 0.653 | |
| 1yob | FMN | Flavodoxin 2 | / | 0.653 | |
| 2c3c | FAD | 2-oxopropyl-CoM reductase, carboxylating | 1.8.1.5 | 0.653 | |
| 2gew | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 2nr4 | FMN | Conserved protein | / | 0.653 | |
| 3sm8 | FNK | FAD-dependent catabolic D-arginine dehydrogenase DauA | / | 0.653 | |
| 4u2t | FAD | Cholesterol oxidase | 1.1.3.6 | 0.653 | |
| 2wp5 | FAD | Trypanothione reductase | / | 0.652 | |
| 1ogj | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.651 | |
| 1xdi | FAD | NAD(P)H dehydrogenase (quinone) | / | 0.651 | |
| 2vyq | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.651 | |
| 5fs6 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.651 | |
| 1akr | FMN | Flavodoxin | / | 0.650 | |
| 1n4v | FAD | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 1que | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.650 | |
| 2r97 | FMN | NAD(P)H dehydrogenase (quinone) | / | 0.650 | |
| 3b6d | FAE | Cholesterol oxidase | 1.1.3.6 | 0.650 | |
| 5fs7 | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.650 |