sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities are compared using Shaper.
For more information, please see the following publication:
Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 1i7p | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 1.000 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.616 | |
| 1umk | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.596 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.568 | |
| 2cnd | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.568 | |
| 1qx4 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.556 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.521 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.518 | |
| 1cne | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.482 | |
| 2i65 | NAD | ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 | 3.2.2.6 | 0.480 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.473 | |
| 4djh | JDC | Kappa-type opioid receptor | / | 0.468 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.467 | |
| 3rpe | FAD | Putative modulator of drug activity | / | 0.467 | |
| 1kbo | 340 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.466 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.466 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.466 | |
| 2x6o | 2TC | Tetracycline repressor protein class D | / | 0.465 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.464 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.463 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.462 | |
| 4m9a | FDA | Acyl-CoA dehydrogenase | / | 0.462 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.461 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.461 | |
| 2aba | STR | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.460 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.459 | |
| 3aty | FMN | Prostaglandin F2a synthase | / | 0.457 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.456 | |
| 2q1u | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.456 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 1tll | FMN | Nitric oxide synthase, brain | 1.14.13.39 | 0.455 | |
| 3eku | CY9 | Actin-5C | / | 0.455 | |
| 4a80 | 2AN | Major pollen allergen Bet v 1-A | / | 0.454 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.452 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.452 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.452 | |
| 2ktd | PUC | Prostaglandin-H2 D-isomerase | 5.3.99.2 | 0.452 | |
| 2rqf | JH3 | Hemolymph juvenile hormone binding protein | / | 0.452 | |
| 4e2d | FMN | Dehydrogenase | / | 0.452 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.451 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.451 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.450 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.450 | |
| 3pft | FMN | Flavin reductase | / | 0.450 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.449 | |
| 1j49 | NAD | D-lactate dehydrogenase | 1.1.1.28 | 0.449 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.449 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.448 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.448 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.448 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.448 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.448 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.447 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 3tqx | PLP | 2-amino-3-ketobutyrate coenzyme A ligase | / | 0.447 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.447 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.447 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.446 | |
| 1q84 | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.446 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.446 | |
| 4jnk | ZHK | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.446 | |
| 4loi | 1YC | Stimulator of interferon genes protein | / | 0.446 | |
| 1f8f | NAD | Benzyl alcohol dehydrogenase | / | 0.445 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.445 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.445 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 3suf | SUE | Polyprotein | / | 0.445 | |
| 4qfy | DCP | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.445 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.444 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.444 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.444 | |
| 3eks | CY9 | Actin-5C | / | 0.444 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.443 | |
| 2wvl | GDD | Mannosyl-3-phosphogylcerate synthase | / | 0.443 | |
| 3h2s | NDP | Putative NADH-flavin reductase | / | 0.443 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.443 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.442 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 2fw3 | BUI | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.442 | |
| 3ai3 | NDP | NADPH-sorbose reductase | / | 0.442 | |
| 3kji | ADP | CO dehydrogenase/acetyl-CoA synthase complex, accessory protein CooC | / | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.442 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.442 | |
| 1qti | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1ydt | IQB | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.441 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.441 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.441 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.441 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.441 | |
| 1a59 | COA | 2-methylcitrate synthase | / | 0.440 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.440 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.440 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.440 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.440 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.440 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4ktk | KTK | Cytochrome P450 | / | 0.440 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.440 | |
| 4ozt | P1A | Ecdysone receptor, putative | / | 0.440 | |
| 5itz | GTP | Tubulin alpha-1B chain | / | 0.440 |