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 |
|---|---|---|---|
| 4j1h | 1HJ | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4j1h | 1HJ | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4j0z | 1H5 | Beta-secretase 1 | 3.4.23.46 | 0.801 | |
| 4bfd | 8T3 | Beta-secretase 1 | 3.4.23.46 | 0.697 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.648 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.623 | |
| 4b1e | 6T6 | Beta-secretase 1 | 3.4.23.46 | 0.621 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.617 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.608 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.605 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.600 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.599 | |
| 4j1i | 1HH | Beta-secretase 1 | 3.4.23.46 | 0.598 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.596 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.595 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.593 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.590 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.590 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.590 | |
| 3rth | RTH | Beta-secretase 1 | 3.4.23.46 | 0.589 | |
| 4fri | DWA | Beta-secretase 1 | 3.4.23.46 | 0.588 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.587 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.585 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.584 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.583 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.582 | |
| 2ohm | 8AP | Beta-secretase 1 | 3.4.23.46 | 0.581 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.579 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.571 | |
| 3rvi | RVI | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 3wb4 | 0B3 | Beta-secretase 1 | 3.4.23.46 | 0.565 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.563 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.562 | |
| 2of0 | CMZ | Beta-secretase 1 | 3.4.23.46 | 0.561 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.559 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.556 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.555 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.554 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.554 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.548 | |
| 3kn0 | 3TO | Beta-secretase 1 | 3.4.23.46 | 0.546 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.542 | |
| 3rtm | RTM | Beta-secretase 1 | 3.4.23.46 | 0.539 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.537 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.534 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.533 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 3l5e | BDW | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 2ohl | 2AQ | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 3l5d | BDV | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 3wb5 | 0B4 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.521 | |
| 3rsv | 3RS | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.518 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 3s2o | EV6 | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 3vv8 | B02 | Beta-secretase 1 | 3.4.23.46 | 0.510 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 2rd2 | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.495 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 3zkn | WZV | Beta-secretase 2 | 3.4.23.45 | 0.489 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 1xva | SAM | Glycine N-methyltransferase | 2.1.1.20 | 0.486 | |
| 3l5b | BDO | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 1qrs | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.483 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 1qtq | QSI | Glutamine--tRNA ligase | 6.1.1.18 | 0.481 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 5dp2 | NAP | CurF | / | 0.473 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4rel | KMP | Glycosyltransferase | / | 0.470 | |
| 4adc | PLP | Succinylornithine transaminase | 2.6.1.81 | 0.468 | |
| 4hmz | 18T | dTDP-4-dehydro-6-deoxyglucose 3-epimerase | 5.1.3.27 | 0.467 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4gid | 0GH | 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 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.453 | |
| 1q5m | NDP | Prostaglandin-E(2) 9-reductase | 1.1.1.189 | 0.452 | |
| 4id9 | NAD | Putative UDP-glucose 4-epimerase | / | 0.452 | |
| 2re8 | GSU | Glutamine--tRNA ligase | 6.1.1.18 | 0.451 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 2anb | 5GP | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2y1w | 849 | Histone-arginine methyltransferase CARM1 | / | 0.448 | |
| 3dyl | PCG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 1s0j | MUS | Trans-sialidase | / | 0.447 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 5c1d | 12V | UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit | / | 0.447 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3a26 | MTA | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.445 | |
| 5c1g | GDU | Histo-blood group ABO system transferase | / | 0.445 | |
| 2a0x | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.444 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3nrr | D16 | Bifunctional dihydrofolate reductase-thymidylate synthase | / | 0.444 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.444 | |
| 1gtr | ATP | Glutamine--tRNA ligase | 6.1.1.18 | 0.443 | |
| 1h60 | STR | Pentaerythritol tetranitrate reductase | / | 0.443 | |
| 3cgt | BCD | Cyclomaltodextrin glucanotransferase | 2.4.1.19 | 0.443 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.441 | |
| 3h2l | YAK | Genome polyprotein | 2.7.7.48 | 0.440 |