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 |
|---|---|---|---|
| 4j1h | 1HJ | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4j1h | 1HJ | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.690 | |
| 4bfd | 8T3 | Beta-secretase 1 | 3.4.23.46 | 0.645 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.630 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.624 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.610 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.603 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.598 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.591 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.584 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.582 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.581 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.579 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.578 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.574 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.574 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.570 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.570 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.561 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.560 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.560 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 2of0 | CMZ | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.556 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 2ohm | 8AP | Beta-secretase 1 | 3.4.23.46 | 0.546 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.538 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.537 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.536 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.534 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.533 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.532 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 3kn0 | 3TO | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.527 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 3wb4 | 0B3 | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 3s2o | EV6 | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 3l5e | BDW | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.508 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 2ohl | 2AQ | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.502 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 3l5d | BDV | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 3rtm | RTM | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.497 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 3wb5 | 0B4 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.489 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.485 | |
| 1qtq | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.484 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 2wjo | QUD | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 5dp2 | NAP | CurF | / | 0.480 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4joo | 1M4 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.476 | |
| 3zkn | WZV | Beta-secretase 2 | 3.4.23.45 | 0.476 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.472 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.471 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.457 | |
| 2y1w | 849 | Histone-arginine methyltransferase CARM1 | / | 0.457 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 2b58 | COA | Diamine acetyltransferase 1 | / | 0.455 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3ske | 054 | Genome polyprotein | 2.7.7.48 | 0.455 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1s0j | MUS | Trans-sialidase | / | 0.453 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.452 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.450 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.450 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.449 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 2h21 | SAM | Ribulose-1,5 bisphosphate carboxylase/oxygenase large subunit N-methyltransferase, chloroplastic | 2.1.1.127 | 0.447 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4twr | NAD | NAD binding site:NAD-dependent epimerase/dehydratase:UDP-glucose 4-epimerase | / | 0.447 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.445 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2xys | SY9 | Soluble acetylcholine receptor | / | 0.445 | |
| 3pdn | SFG | Histone-lysine N-methyltransferase SMYD3 | 2.1.1.43 | 0.445 | |
| 2g1a | 5HG | Class B acid phosphatase | 3.1.3.2 | 0.444 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 3cow | 52H | Pantothenate synthetase | 6.3.2.1 | 0.444 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.443 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.443 | |
| 3g45 | 988 | cAMP-specific 3',5'-cyclic phosphodiesterase 4B | 3.1.4.53 | 0.443 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4f4d | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.443 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.442 | |
| 1q0r | AKT | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.442 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.442 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.441 | |
| 1qrs | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.440 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.440 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.440 |