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 |
|---|---|---|---|
| 4b1d | 6TG | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4b1d | 6TG | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.637 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.632 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.624 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.606 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.604 | |
| 3l5d | BDV | Beta-secretase 1 | 3.4.23.46 | 0.583 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.581 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 3rtm | RTM | Beta-secretase 1 | 3.4.23.46 | 0.570 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.568 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.560 | |
| 3s2o | EV6 | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 4joo | 1M4 | Beta-secretase 1 | 3.4.23.46 | 0.549 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.545 | |
| 4jp9 | 1M5 | Beta-secretase 1 | 3.4.23.46 | 0.541 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.537 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.535 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.535 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 3l5e | BDW | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.514 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.506 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 2ohl | 2AQ | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 2vpr | TDC | Tetracycline repressor protein class H | / | 0.475 | |
| 4j1i | 1HH | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.471 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3dyn | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.464 | |
| 4b14 | 4XB | Glycylpeptide N-tetradecanoyltransferase | / | 0.464 | |
| 2rhr | EMO | Putative ketoacyl reductase | 1.3.1 | 0.463 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.462 | |
| 2a1h | GBN | Branched-chain-amino-acid aminotransferase, mitochondrial | 2.6.1.42 | 0.462 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.462 | |
| 1h22 | E10 | Acetylcholinesterase | 3.1.1.7 | 0.461 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.455 | |
| 1b2l | NDC | Alcohol dehydrogenase | 1.1.1.1 | 0.454 | |
| 2qe2 | 452 | Polyprotein | / | 0.453 | |
| 3zky | WT4 | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3dys | IBM | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3ehe | NAD | UDP-glucose 4-epimerase (GalE-1) | / | 0.452 | |
| 1m9n | AMZ | Bifunctional purine biosynthesis protein PURH | 2.1.2.3 | 0.450 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.450 | |
| 4zzi | 1NS | NAD-dependent protein deacetylase sirtuin-1 | 3.5.1 | 0.450 | |
| 1gpn | HUB | Acetylcholinesterase | 3.1.1.7 | 0.449 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.449 | |
| 4gh6 | LUO | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2ejz | SAH | Diphthine synthase | / | 0.445 | |
| 1rzu | ADP | Glycogen synthase 1 | 2.4.1.21 | 0.444 | |
| 1lke | DOG | Bilin-binding protein | / | 0.443 | |
| 1eno | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic | 1.3.1.9 | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1obn | ASV | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 1pd9 | CO4 | Dihydrofolate reductase | 1.5.1.3 | 0.441 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.441 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.441 | |
| 4ey6 | GNT | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 1rt9 | IMH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.440 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.440 | |
| 3muo | ZPR | Prolyl endopeptidase | / | 0.440 |