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 Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 3aty | FMN | Prostaglandin F2a synthase |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3aty | FMN | Prostaglandin F2a synthase | / | 1.000 | |
| 4e2b | FMN | Dehydrogenase | / | 0.674 | |
| 4e2d | FMN | Dehydrogenase | / | 0.665 | |
| 3atz | FMN | Prostaglandin F2a synthase | / | 0.660 | |
| 4jic | FMN | GTN Reductase | / | 0.552 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.549 | |
| 1h50 | FMN | Pentaerythritol tetranitrate reductase | / | 0.532 | |
| 4rnu | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.530 | |
| 1h63 | FMN | Pentaerythritol tetranitrate reductase | / | 0.527 | |
| 3hgo | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.527 | |
| 1vyr | FMN | Pentaerythritol tetranitrate reductase | / | 0.524 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.520 | |
| 2hs8 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.513 | |
| 3p74 | FMN | Pentaerythritol tetranitrate reductase | / | 0.512 | |
| 3p82 | FMN | Pentaerythritol tetranitrate reductase | / | 0.512 | |
| 2abb | FMN | Pentaerythritol tetranitrate reductase | / | 0.509 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.509 | |
| 4a3u | FMN | NADH:flavin oxidoreductase/NADH oxidase | / | 0.509 | |
| 3hgs | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.507 | |
| 1q45 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.506 | |
| 1icq | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.500 | |
| 4tmb | FMN | Old yellow enzyme | / | 0.500 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.498 | |
| 2q3r | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.498 | |
| 5a4k | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.498 | |
| 1gg5 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.495 | |
| 1h51 | FMN | Pentaerythritol tetranitrate reductase | / | 0.495 | |
| 1kbo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.495 | |
| 4ewn | 0VR | Imidazole glycerol phosphate synthase subunit HisF | 4.1.3 | 0.494 | |
| 1icp | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.492 | |
| 1bwl | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.490 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.489 | |
| 3hgr | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.487 | |
| 1h66 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.485 | |
| 1vji | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.484 | |
| 4c7k | NAP | Corticosteroid 11-beta-dehydrogenase isozyme 1 | 1.1.1.146 | 0.483 | |
| 1h69 | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.482 | |
| 4tmc | FMN | Old yellow enzyme | / | 0.482 | |
| 1kbq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.481 | |
| 4h6k | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.478 | |
| 2f1k | NAP | Prephenate dehydrogenase | / | 0.477 | |
| 4rnv | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.477 | |
| 3gka | FMN | N-ethylmaleimide reductase | / | 0.476 | |
| 1ics | FMN | 12-oxophytodienoate reductase 1 | 1.3.1.42 | 0.475 | |
| 4df2 | FMN | NADPH dehydrogenase | / | 0.475 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.474 | |
| 4r81 | FMN | Predicted NADH dehydrogenase | / | 0.472 | |
| 2cmj | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.470 | |
| 2fzw | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.470 | |
| 3rud | NAD | UDP-N-acetylglucosamine 4-epimerase | / | 0.470 | |
| 3p84 | FMN | Pentaerythritol tetranitrate reductase | / | 0.469 | |
| 3p8i | FMN | Pentaerythritol tetranitrate reductase | / | 0.468 | |
| 1dxo | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.467 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.466 | |
| 3gfb | NAD | L-threonine 3-dehydrogenase | / | 0.466 | |
| 1bws | NDP | GDP-L-fucose synthase | / | 0.464 | |
| 1oyc | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.464 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.462 | |
| 5eai | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.462 | |
| 2rcy | NAP | Pyrroline-5-carboxylate reductase | / | 0.461 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.461 | |
| 1u7t | NAD | 3-hydroxyacyl-CoA dehydrogenase type-2 | 1.1.1.35 | 0.460 | |
| 4ge7 | 0K5 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.460 | |
| 3in6 | FMN | Uncharacterized protein | / | 0.459 | |
| 3p8j | FMN | Pentaerythritol tetranitrate reductase | / | 0.459 | |
| 3to6 | LYS_CMC | Histone acetyltransferase ESA1 | / | 0.459 | |
| 1dxq | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.458 | |
| 3etd | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.458 | |
| 2c3q | GTX | Glutathione S-transferase theta-1 | 2.5.1.18 | 0.457 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.457 | |
| 1o0s | NAI | NAD-dependent malic enzyme, mitochondrial | 1.1.1.38 | 0.456 | |
| 2w9s | TOP | Dihydrofolate reductase type 1 from Tn4003 | 1.5.1.3 | 0.456 | |
| 3cty | FAD | Probable thioredoxin reductase | / | 0.456 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.455 | |
| 4z3d | NDP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.455 | |
| 2jn3 | JN3 | Fatty acid-binding protein, liver | / | 0.454 | |
| 3r5y | F42 | Uncharacterized protein | / | 0.454 | |
| 1t0l | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.453 | |
| 2hs6 | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.453 | |
| 4q73 | FAD | Bifunctional protein PutA | / | 0.453 | |
| 1zdw | FLV | Prenyltransferase | / | 0.452 | |
| 2wyv | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.451 | |
| 2y0m | ACO | Histone acetyltransferase KAT8 | / | 0.451 | |
| 4fw8 | NAI | 3-oxoacyl-(Acyl-carrier-protein) reductase | / | 0.451 | |
| 1e3e | NAI | Alcohol dehydrogenase 4 | 1.1.1.1 | 0.450 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.450 | |
| 3flk | NAI | Tartrate dehydrogenase/decarboxylase | 1.1.1.93 | 0.450 | |
| 3flw | FLW | Mitogen-activated protein kinase 14 | / | 0.450 | |
| 3sz0 | FAD | Sulfide-quinone reductase | / | 0.450 | |
| 2j3i | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.449 | |
| 2p5u | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 3tqh | NDP | Quinone oxidoreductase | / | 0.449 | |
| 3uko | NAD | Alcohol dehydrogenase class-3 | / | 0.449 | |
| 4h8a | NAI | Ureidoglycolate dehydrogenase (NAD(+)) | 1.1.1.350 | 0.449 | |
| 4jbi | NDP | Alcohol dehydrogenase (Zinc) | / | 0.449 | |
| 5a3b | APR | SIR2 family protein | / | 0.449 | |
| 5dp2 | NAP | CurF | / | 0.449 | |
| 1g4t | FTP | Thiamine-phosphate synthase | / | 0.448 | |
| 1kr2 | TAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 1 | 2.7.7.1 | 0.448 | |
| 1oya | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.448 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.448 | |
| 3t2z | FAD | Sulfide-quinone reductase | / | 0.448 | |
| 1mp0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.447 | |
| 2a92 | NAI | L-lactate dehydrogenase | / | 0.447 | |
| 2g5c | NAD | Prephenate dehydrogenase | / | 0.447 | |
| 2q3o | FMN | 12-oxophytodienoate reductase 3 | 1.3.1.42 | 0.447 | |
| 3f1k | NAP | Uncharacterized oxidoreductase YciK | 1 | 0.447 | |
| 1ipe | NDP | Tropinone reductase 2 | 1.1.1.236 | 0.446 | |
| 1ma0 | NAD | Alcohol dehydrogenase class-3 | 1.1.1.1 | 0.446 | |
| 2ft9 | CHD | Fatty acid-binding protein 2, liver | / | 0.446 | |
| 2ztv | NAD | D(-)-3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 3fpa | DTB | ATP-dependent dethiobiotin synthetase BioD | / | 0.446 | |
| 1gqt | ACP | Ribokinase | / | 0.445 | |
| 1iol | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.445 | |
| 3a1n | NAD | NDP-sugar epimerase | / | 0.445 | |
| 3etg | NDP | Glutamate dehydrogenase 1, mitochondrial | 1.4.1.3 | 0.445 | |
| 3och | 2MX | Dihydrofolate reductase | 1.5.1.3 | 0.445 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.445 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.445 | |
| 2j3k | NAP | NADPH-dependent oxidoreductase 2-alkenal reductase | 1.3.1.74 | 0.444 | |
| 3bhi | NAP | Carbonyl reductase [NADPH] 1 | 1.1.1.184 | 0.444 | |
| 3coy | 53H | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 3oet | NAD | Erythronate-4-phosphate dehydrogenase | / | 0.444 | |
| 2ou2 | ACO | Histone acetyltransferase KAT5 | / | 0.443 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.443 | |
| 3tox | NAP | Putative oxidoreductase | / | 0.443 | |
| 4dja | FAD | (6-4) photolyase | / | 0.443 | |
| 4irn | FAD | AnaB | / | 0.443 | |
| 4k7y | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.443 | |
| 4m5p | FMN | NADPH dehydrogenase | / | 0.443 | |
| 4yry | FAD | Glutamate synthase, beta subunit | / | 0.443 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.442 | |
| 1yb5 | NAP | Quinone oxidoreductase | 1.6.5.5 | 0.442 | |
| 3inm | NDP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.442 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.442 | |
| 4bv9 | NDP | Ketimine reductase mu-crystallin | 1.5.1.25 | 0.442 | |
| 4xw4 | ANP | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.442 | |
| 5a3c | NAD | SIR2 family protein | / | 0.442 | |
| 2hay | FMN | Putative NAD(P)H-flavin oxidoreductase | / | 0.441 | |
| 2xpu | TDC | Tetracycline repressor protein class D | / | 0.441 | |
| 3gy0 | NAP | NAD(P)-dependent oxidoreductase | / | 0.441 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.441 | |
| 4l03 | NAP | Isocitrate dehydrogenase [NADP] cytoplasmic | 1.1.1.42 | 0.441 | |
| 2fj1 | CTC | Tetracycline repressor protein class D | / | 0.440 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.440 | |
| 2rgh | FAD | Alpha-Glycerophosphate Oxidase | / | 0.440 | |
| 3ggg | NAD | Prephenate dehydrogenase | / | 0.440 | |
| 3pw8 | ACO | 1,2-phenylacetyl-CoA epoxidase, subunit A | 1.14.13.149 | 0.440 | |
| 4amb | DUD | Putative glycosyl transferase | / | 0.440 |