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 |
|---|---|---|---|
| 3gr8 | FMN | NADPH dehydrogenase |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3gr8 | FMN | NADPH dehydrogenase | / | 1.000 | |
| 3kru | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.576 | |
| 3hf3 | FMN | Chromate reductase | / | 0.569 | |
| 1z48 | FMN | NADPH dehydrogenase | / | 0.561 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.557 | |
| 1z44 | FMN | NADPH dehydrogenase | / | 0.550 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.538 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.537 | |
| 1z41 | FMN | NADPH dehydrogenase | / | 0.532 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.532 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.527 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.523 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.509 | |
| 2gou | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.509 | |
| 3l5l | FMN | Xenobiotic reductase | / | 0.508 | |
| 4qnw | FMN | Chanoclavine-I aldehyde reductase easA | / | 0.507 | |
| 3tjl | FMN | NADPH dehydrogenase | / | 0.506 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.502 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.498 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.497 | |
| 2h8x | FMN | XenA | / | 0.493 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.491 | |
| 3b05 | IPE | Isopentenyl-diphosphate delta-isomerase | / | 0.490 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.489 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.489 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.487 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.487 | |
| 1d0l | BLG | Membrane-bound lytic murein transglycosylase B | 4.2.2.n1 | 0.486 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.486 | |
| 4rnw | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.486 | |
| 3b05 | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.485 | |
| 2zrv | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.483 | |
| 3bxo | UPP | dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose | / | 0.483 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.482 | |
| 2zry | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.481 | |
| 2zrz | FNR | Isopentenyl-diphosphate delta-isomerase | / | 0.480 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.480 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.479 | |
| 3b03 | VNR | Isopentenyl-diphosphate delta-isomerase | / | 0.475 | |
| 4ycp | FMN | tRNA-dihydrouridine(16) synthase | / | 0.475 | |
| 4yl2 | FMN | Lactate oxidase | / | 0.475 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.474 | |
| 1kbi | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.473 | |
| 4awt | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.473 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.471 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.471 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.471 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.470 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.470 | |
| 4uth | FMN | Xenobiotic reductase | / | 0.470 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.469 | |
| 4qai | FMN | NADPH dehydrogenase | / | 0.469 | |
| 2ed3 | SAH | Diphthine synthase | / | 0.468 | |
| 2ejz | SAH | Diphthine synthase | / | 0.468 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 4utk | FNR | Xenobiotic reductase | / | 0.468 | |
| 4aws | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.467 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.466 | |
| 3il1 | B5D | Glutamate receptor 2 | / | 0.466 | |
| 4b5n | FMN | NAD(P)H:flavin oxidoreductase Sye4 | / | 0.466 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.465 | |
| 3b04 | OOP | Isopentenyl-diphosphate delta-isomerase | / | 0.464 | |
| 3ime | BZ2 | Pantothenate synthetase | 6.3.2.1 | 0.464 | |
| 4xnw | 2ID | P2Y purinoceptor 1 | / | 0.464 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.463 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.463 | |
| 2q1w | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.463 | |
| 4wpu | GDP | Phosphoenolpyruvate carboxykinase [GTP] | / | 0.463 | |
| 1w0k | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.462 | |
| 1w0k | ADP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.462 | |
| 2vnj | FAD | NADPH:ferredoxin reductase | / | 0.461 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.461 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.460 | |
| 3clu | FAD | Electron transfer flavoprotein subunit alpha | / | 0.460 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.460 | |
| 3zhr | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.460 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4dyn | 0MR | Nucleoprotein | / | 0.460 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.460 | |
| 4rje | FNR | Lactate oxidase | / | 0.460 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.459 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.459 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.459 | |
| 2gqa | FMN | NADH:flavin oxidoreductase Sye1 | / | 0.459 | |
| 2qbu | SAH | Precorrin-2 methyltransferase | / | 0.459 | |
| 2zrx | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.459 | |
| 3i0p | NAD | Malate dehydrogenase, putative | / | 0.459 | |
| 4f97 | VDO | Putative glycosyltransferase | / | 0.459 | |
| 4w5k | PLP | Aspartate aminotransferase, mitochondrial | / | 0.459 | |
| 1kbj | FMN | Cytochrome b2, mitochondrial | 1.1.2.3 | 0.458 | |
| 4wec | NAD | Short chain dehydrogenase | / | 0.458 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.457 | |
| 1xel | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.457 | |
| 2b3d | FAD | Modulator of drug activity B | / | 0.457 | |
| 4e2d | FMN | Dehydrogenase | / | 0.457 | |
| 4rvd | SAM | D-mycarose 3-C-methyltransferase | / | 0.457 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.456 | |
| 2ejv | NAD | L-threonine 3-dehydrogenase | / | 0.456 | |
| 2ohj | FMN | Type A flavoprotein FprA | 1 | 0.456 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.456 | |
| 4rnx | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.456 | |
| 1fml | RTL | Retinol dehydratase | / | 0.455 | |
| 1n0s | FLU | Bilin-binding protein | / | 0.455 | |
| 1t9g | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.455 | |
| 2dfv | NAD | L-threonine 3-dehydrogenase | / | 0.455 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.455 | |
| 3aez | GDP | Pantothenate kinase | 2.7.1.33 | 0.455 | |
| 3fwg | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.455 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.455 | |
| 3q9b | B3N | Acetylpolyamine amidohydrolase | / | 0.455 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.454 | |
| 1vhn | FMN | tRNA-dihydrouridine synthase | / | 0.454 | |
| 3b4y | F42 | F420-dependent glucose-6-phosphate dehydrogenase | / | 0.454 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.454 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.453 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 2i7p | ACO | Pantothenate kinase 3 | 2.7.1.33 | 0.453 | |
| 3ing | NDP | Homoserine dehydrogenase related protein | / | 0.453 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.453 | |
| 3tr0 | 5GP | Guanylate kinase | / | 0.453 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.452 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.452 | |
| 2o1s | TDP | 1-deoxy-D-xylulose-5-phosphate synthase | 2.2.1.7 | 0.452 | |
| 3axk | NDP | Ribulose bisphosphate carboxylase large chain | 4.1.1.39 | 0.452 | |
| 2j2p | SC2 | Ficolin-2 | / | 0.451 | |
| 2p9g | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.451 | |
| 3hdh | NAD | Hydroxyacyl-coenzyme A dehydrogenase, mitochondrial | 1.1.1.35 | 0.451 | |
| 4ddh | MS0 | Pantothenate synthetase | 6.3.2.1 | 0.451 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.450 | |
| 1g7v | PAI | 2-dehydro-3-deoxyphosphooctonate aldolase | 2.5.1.55 | 0.450 | |
| 1gpu | THD | Transketolase 1 | 2.2.1.1 | 0.450 | |
| 1h74 | ADP | Homoserine kinase | 2.7.1.39 | 0.450 | |
| 1kvu | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.450 | |
| 2oc9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.450 | |
| 2v2z | ADP | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.450 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit alpha | 1.2.4.1 | 0.450 | |
| 3dva | TPW | Pyruvate dehydrogenase E1 component subunit beta | 1.2.4.1 | 0.450 | |
| 3e39 | FMN | Nitroreductase | / | 0.450 | |
| 3fr5 | I4A | Fatty acid-binding protein, adipocyte | / | 0.450 | |
| 3m2v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.450 | |
| 1hyg | NAP | L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+)) | / | 0.449 | |
| 1kvs | UPG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.449 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.449 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.449 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.449 | |
| 1ay0 | TPP | Transketolase 1 | 2.2.1.1 | 0.448 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 3eks | CY9 | Actin-5C | / | 0.448 | |
| 3r96 | ACO | MccE protein | / | 0.448 | |
| 3s8p | SAM | Histone-lysine N-methyltransferase KMT5B | 2.1.1.43 | 0.448 | |
| 4bzb | DGT | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | 3.1.5 | 0.448 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.448 | |
| 4eqr | COA | Coenzyme A disulfide reductase | / | 0.448 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.448 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2feu | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.447 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.447 | |
| 2zsa | ADP | Pantothenate kinase | 2.7.1.33 | 0.447 | |
| 3akz | GSU | Glutamate--tRNA ligase 2 | / | 0.447 | |
| 4mv1 | ADP | Biotin carboxylase | 6.3.4.14 | 0.447 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.447 | |
| 5a0y | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.447 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.446 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 4dpy | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.446 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.446 | |
| 2qf2 | GDP | Phosphoenolpyruvate carboxykinase, cytosolic [GTP] | 4.1.1.32 | 0.445 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.445 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1itz | TPP | Transketolase, chloroplastic | 2.2.1.1 | 0.444 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.444 | |
| 2c6c | 24I | Glutamate carboxypeptidase 2 | 3.4.17.21 | 0.444 | |
| 2du2 | FMN | Lactate oxidase | / | 0.444 | |
| 2p9c | NAI | D-3-phosphoglycerate dehydrogenase | 1.1.1.95 | 0.444 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.444 | |
| 2w6q | OA5 | Biotin carboxylase | 6.3.4.14 | 0.444 | |
| 2znn | S44 | Peroxisome proliferator-activated receptor alpha | / | 0.444 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.444 | |
| 3m1v | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.444 | |
| 3qvi | K95 | HAP protein | / | 0.444 | |
| 3toz | NAD | Shikimate dehydrogenase (NADP(+)) | / | 0.444 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.444 | |
| 3otb | DGT | Probable tRNA(His) guanylyltransferase | 2.7.7.79 | 0.443 | |
| 3tri | NAP | Pyrroline-5-carboxylate reductase | / | 0.443 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.443 | |
| 4fhd | 0TT | Spore photoproduct lyase | / | 0.443 | |
| 5b0o | ADP | Flagellum-specific ATP synthase | 3.6.3.14 | 0.443 | |
| 1ftl | DNQ | Glutamate receptor 2 | / | 0.442 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.442 | |
| 2a0y | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.442 | |
| 2a5h | SAM | L-lysine 2,3-aminomutase | 5.4.3.2 | 0.442 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.442 | |
| 3ko8 | NAD | NAD-dependent epimerase/dehydratase | / | 0.442 | |
| 3ojx | FMN | NADPH--cytochrome P450 reductase | / | 0.442 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.442 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 4ead | 0NP | Thymidine phosphorylase | 2.4.2.4 | 0.442 | |
| 4lcj | NAD | C-terminal-binding protein 2 | / | 0.442 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.442 | |
| 4wh3 | ATP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.442 | |
| 4z4p | SAH | Histone-lysine N-methyltransferase 2D | 2.1.1.43 | 0.442 | |
| 6cp4 | CAM | Camphor 5-monooxygenase | 1.14.15.1 | 0.442 | |
| 1a8p | FAD | Ferredoxin--NADP reductase | / | 0.441 | |
| 2g25 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.441 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.441 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.441 | |
| 3o03 | NAP | Dehydrogenase with different specificities (Related to short-chain alcohol dehydrogenase) | / | 0.441 | |
| 3ziu | LSS | Leucyl-tRNA synthetase | / | 0.441 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.441 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.441 | |
| 5bt9 | NAP | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.441 | |
| 5e8j | SAH | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.441 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.441 | |
| 1e79 | ATP | ATP synthase subunit alpha, mitochondrial | / | 0.440 | |
| 1e79 | ATP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.440 | |
| 1g9d | BAB | Botulinum neurotoxin type B | 3.4.24.69 | 0.440 | |
| 1p4a | PCP | Pur operon repressor | / | 0.440 | |
| 1s63 | 778 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 1sa4 | JAN | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 2jcx | NDP | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | / | 0.440 | |
| 2qta | TDP | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3b6z | CO7 | Enoyl reductase LovC | 1 | 0.440 | |
| 3e32 | ED2 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.440 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.440 | |
| 3hml | PQQ | Pyrroloquinoline-quinone synthase | / | 0.440 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit alpha | 2.8.4.1 | 0.440 | |
| 3m30 | COM | Methyl-coenzyme M reductase I subunit beta | 2.8.4.1 | 0.440 | |
| 3n19 | FNR | Xenobiotic reductase | / | 0.440 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.440 | |
| 4c8e | C5P | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | / | 0.440 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4g74 | FAD | Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial | 1.6.5.9 | 0.440 | |
| 4hmv | WUB | Phenazine biosynthesis protein PhzG | 1.4 | 0.440 | |
| 4l8u | 9AZ | Serum albumin | / | 0.440 |