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 |
|---|---|---|---|
| 2ohr | 8IP | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 2ohr | 8IP | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 | 0.674 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.586 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.584 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.579 | |
| 2ohp | 6IP | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 2ohu | IP7 | Beta-secretase 1 | 3.4.23.46 | 0.568 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.556 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 4i11 | 1CH | Beta-secretase 1 | 3.4.23.46 | 0.545 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.543 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.542 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.541 | |
| 4i12 | 1BC | Beta-secretase 1 | 3.4.23.46 | 0.536 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.534 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 4jp9 | 1M5 | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.513 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.506 | |
| 3bug | AEH | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 2of0 | CMZ | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.485 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.483 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 3c1o | NAP | Eugenol synthase | / | 0.478 | |
| 4joo | 1M4 | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.474 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.474 | |
| 1hfq | MOT | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3l5e | BDW | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.470 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.469 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.466 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2ohm | 8AP | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3gwf | FAD | Cyclohexanone monooxygenase | / | 0.464 | |
| 1bp6 | UMP | Thymidylate synthase | / | 0.462 | |
| 1vzd | CB3 | Thymidylate synthase | / | 0.462 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3em0 | CHD | Fatty acid-binding protein 6, ileal (gastrotropin) | / | 0.461 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 3p67 | FMN | Pentaerythritol tetranitrate reductase | / | 0.460 | |
| 3zv7 | NHG | Acetylcholinesterase | 3.1.1.7 | 0.459 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.459 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.458 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.458 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.457 | |
| 2oci | TYC | Valacyclovir hydrolase | 3.1 | 0.457 | |
| 2yig | 5EL | Collagenase 3 | 3.4.24 | 0.457 | |
| 4dro | 0MD | Peptidyl-prolyl cis-trans isomerase FKBP5 | 5.2.1.8 | 0.457 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 4qmp | DKI | Serine/threonine-protein kinase 24 | 2.7.11.1 | 0.455 | |
| 2rh9 | IGP | Tryptophan synthase alpha chain | / | 0.454 | |
| 1cne | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.453 | |
| 2vrj | NCW | Beta-glucosidase A | 3.2.1.21 | 0.453 | |
| 2cjf | RP4 | 3-dehydroquinate dehydratase | 4.2.1.10 | 0.451 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 3i8p | 840 | 3-oxoacyl-[acyl-carrier-protein] synthase 2 | 2.3.1.179 | 0.451 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.450 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.450 | |
| 2v5a | LZL | Biotin carboxylase | 6.3.4.14 | 0.450 | |
| 1dd6 | MCI | Metallo-beta-lactamase type 2 | / | 0.449 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 1pfy | MSP | Methionine--tRNA ligase | 6.1.1.10 | 0.448 | |
| 1qh0 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.448 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 1xom | CIO | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.447 | |
| 2emu | SAH | Diphthine synthase | / | 0.447 | |
| 2zjn | F1N | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3d28 | B34 | Genome polyprotein | 2.7.7.48 | 0.447 | |
| 3uax | NOS | Purine nucleoside phosphorylase DeoD-type | / | 0.447 | |
| 3up0 | D7S | aceDAF-12 | / | 0.447 | |
| 4dc0 | NDP | Putative ketoacyl reductase | 1.3.1 | 0.447 | |
| 4gz6 | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.447 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.446 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.446 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.445 | |
| 4mv8 | ACP | Biotin carboxylase | 6.3.4.14 | 0.445 | |
| 1g63 | FMN | Epidermin decarboxylase | 4.1.1 | 0.444 | |
| 2oht | IP6 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3h7r | NAP | Aldo-keto reductase family 4 member C8 | / | 0.444 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.444 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 1ci7 | UMP | Thymidylate synthase | 2.1.1.45 | 0.443 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.443 | |
| 1fnc | FDA | Ferredoxin--NADP reductase, chloroplastic | 1.18.1.2 | 0.443 | |
| 2dsg | SAH | Diphthine synthase | / | 0.443 | |
| 2w6o | OA3 | Biotin carboxylase | 6.3.4.14 | 0.443 | |
| 3e8e | G98 | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4b63 | NAP | L-ornithine N(5)-monooxygenase | / | 0.443 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.443 | |
| 1dnp | MHF | Deoxyribodipyrimidine photo-lyase | 4.1.99.3 | 0.442 | |
| 1fds | EST | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.442 | |
| 1osv | CHC | Bile acid receptor | / | 0.442 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.442 | |
| 3dop | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.442 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.442 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.442 | |
| 3wb4 | 0B3 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.441 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4ure | 1PS | Cyclohexanol dehydrogenase | / | 0.441 | |
| 1tsx | UMP | Thymidylate synthase | / | 0.440 | |
| 1ywg | NAD | Glyceraldehyde-3-phosphate dehydrogenase | / | 0.440 | |
| 2v3w | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.440 | |
| 2v58 | LZJ | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 3zc3 | FAD | Ferredoxin--NADP reductase | 1.18.1.2 | 0.440 |