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 |
|---|---|---|---|
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 1nec | FMN | Oxygen-insensitive NAD(P)H nitroreductase | 1 | 1.274 | |
| 1kqb | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.239 | |
| 1yki | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.232 | |
| 1ylr | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.232 | |
| 1icu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.229 | |
| 1kqc | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.226 | |
| 1oon | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.226 | |
| 1kqd | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.209 | |
| 1ooq | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.170 | |
| 1oo5 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.150 | |
| 1icv | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.140 | |
| 3x22 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.118 | |
| 1ylu | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.100 | |
| 1ds7 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.096 | |
| 1vfr | FMN | Major NAD(P)H-flavin oxidoreductase | 1.6.99 | 1.059 | |
| 3x21 | FMN | Oxygen-insensitive NAD(P)H nitroreductase | / | 1.033 | |
| 2wzv | FMN | Nitroreductase NfnB | / | 0.958 | |
| 2wzw | FMN | Nitroreductase NfnB | / | 0.953 | |
| 3koq | FMN | Putative nitroreductase | / | 0.950 | |
| 3ge6 | FMN | Nitroreductase | / | 0.946 | |
| 3qdl | FMN | Oxygen-insensitive NADPH nitroreductase | / | 0.889 | |
| 3pxv | FMN | Nitroreductase | / | 0.888 | |
| 3of4 | FMN | Nitroreductase | / | 0.877 | |
| 3gag | FMN | Putative NADH dehydrogenase NAD(P)H nitroreductase | / | 0.862 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.847 | |
| 3bem | FMN | Putative NAD(P)H nitroreductase MhqN | 1 | 0.815 | |
| 2fre | FMN | NAD(P)H-flavin oxidoreductase | / | 0.789 | |
| 2isl | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.775 | |
| 4qly | FMN | Enone reductase CLA-ER | / | 0.772 | |
| 4eo3 | FMN | Bacterioferritin comigratory protein/NADH dehydrogenase | / | 0.755 | |
| 3hj9 | FMN | Uncharacterized protein | / | 0.734 | |
| 4ttb | FMN | Iodotyrosine deiodinase 1 | / | 0.733 | |
| 3e39 | FMN | Nitroreductase | / | 0.730 | |
| 4y9l | FAD | Acyl-CoA dehydrogenase family member 11 | / | 0.724 | |
| 3eo8 | FMN | Putative nitroreductase | / | 0.721 | |
| 3gdp | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.715 | |
| 2isj | FMN | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.712 | |
| 4xoo | FMN | Coenzyme F420:L-glutamate ligase | / | 0.712 | |
| 2bkj | FMN | NADPH-flavin oxidoreductase | / | 0.706 | |
| 3gh8 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.704 | |
| 2i51 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.703 | |
| 3e4v | FMN | Uncharacterized protein | / | 0.702 | |
| 4hnb | FMN | LOV protein | / | 0.700 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.696 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.694 | |
| 2i02 | FMN | Pyridoxamine 5'-phosphate oxidase-related, FMN-binding | / | 0.687 | |
| 2hq9 | FAD | Mll6688 protein | / | 0.684 | |
| 3gfd | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.684 | |
| 4wqm | FAD | Toluene-4-monooxygenase electron transfer component | 1.18.1.3 | 0.680 | |
| 4ttc | FMN | Iodotyrosine deiodinase 1 | / | 0.677 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.674 | |
| 5j3w | FMN | Sensory box protein | / | 0.671 | |
| 2isk | FNR | 5,6-dimethylbenzimidazole synthase | 1.13.11.79 | 0.670 | |
| 3a3b | RBF | Lumazine protein | / | 0.670 | |
| 3dga | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.670 | |
| 4d7e | FAD | Putative lysine-N-oxygenase | / | 0.668 | |
| 4hhd | FMN | Phototropin-1 | 2.7.11.1 | 0.667 | |
| 1tyt | FAD | Trypanothione reductase | 1.8.1.12 | 0.663 | |
| 2ed4 | FAD | 4-hydroxyphenylacetate 3-monooxygenase reductase component | 1.5.1.36 | 0.662 | |
| 2z1q | FAD | Acyl-CoA dehydrogenase | / | 0.662 | |
| 3to0 | FMN | Iodotyrosine deiodinase 1 | 1.21.1.1 | 0.661 | |
| 4iil | RBF | Membrane lipoprotein TpN38(b) | / | 0.659 | |
| 4nmd | FDA | Bifunctional protein PutA | / | 0.659 | |
| 1x31 | FMN | Subunit alpha of sarocosine oxidase | / | 0.657 | |
| 1x31 | FMN | Subunit beta of sarcosine oxidase | / | 0.657 | |
| 3clt | FAD | Electron transfer flavoprotein subunit alpha | / | 0.657 | |
| 3ez3 | ZOL | Farnesyl pyrophosphate synthase, putative | / | 0.657 | |
| 1rz0 | FAD | Phenol 2-hydroxylase component B | / | 0.656 | |
| 1t0i | FMN | NAD(P)H-dependent FMN reductase LOT6 | / | 0.656 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.656 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.655 | |
| 1qlt | FAD | Vanillyl-alcohol oxidase | 1.1.3.38 | 0.654 | |
| 3oib | FDA | Putative acyl-CoA dehydrogenase | / | 0.653 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.652 | |
| 1g4p | FQP | Thiamine-phosphate synthase | / | 0.650 | |
| 1p4m | FMN | Riboflavin kinase | 2.7.1.26 | 0.650 | |
| 2q4w | FAD | Cytokinin dehydrogenase 7 | 1.5.99.12 | 0.650 | |
| 4b8w | GDP | GDP-L-fucose synthase | 1.1.1.271 | 0.650 |