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 |
|---|---|---|---|
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.586 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.585 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.580 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.578 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.577 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.576 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.571 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.570 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.569 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.567 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.565 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.561 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.560 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.558 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.553 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.551 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.551 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.550 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.544 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.542 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.537 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.536 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.535 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.535 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.534 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.534 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.533 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.527 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.527 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.526 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.526 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.524 | |
| 2iku | LIY | Renin | 3.4.23.15 | 0.524 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.515 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.512 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.510 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.510 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.510 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.509 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.508 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.506 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.506 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.506 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.503 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.498 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.498 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.497 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.494 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.494 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.493 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 3zkn | WZV | Beta-secretase 2 | 3.4.23.45 | 0.491 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.489 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 3l5d | BDV | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.487 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.484 | |
| 3n4l | 842 | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.483 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.483 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.481 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.478 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.477 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.475 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.475 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.475 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.474 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.473 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.472 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.470 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.470 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 3oag | LPQ | Renin | 3.4.23.15 | 0.468 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.468 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 4joo | 1M4 | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 3oad | LPO | Renin | 3.4.23.15 | 0.464 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.464 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.463 | |
| 3q70 | RIT | Candidapepsin-2 | 3.4.23.24 | 0.463 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.462 | |
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3l5e | BDW | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 2fs4 | PZ1 | Renin | 3.4.23.15 | 0.460 | |
| 3oee | ANP | ATP synthase subunit alpha, mitochondrial | / | 0.460 | |
| 3oee | ANP | ATP synthase subunit beta, mitochondrial | 3.6.3.14 | 0.460 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.459 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.459 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.458 | |
| 3qj0 | QI3 | Botulinum neurotoxin type A | 3.4.24.69 | 0.458 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4dus | 0MP | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.457 | |
| 3udj | 092 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4fsl | 0VB | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.453 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 4l7h | 1W1 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.451 | |
| 2g27 | 4LG | Renin | 3.4.23.15 | 0.451 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.450 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.449 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.449 | |
| 3wb4 | 0B3 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4eso | NAP | Putative oxidoreductase | / | 0.449 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.448 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.448 | |
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.448 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.447 | |
| 3g70 | A5T | Renin | 3.4.23.15 | 0.445 | |
| 3qiz | QI2 | Botulinum neurotoxin type A | 3.4.24.69 | 0.445 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.444 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2yoj | 8Y6 | Genome polyprotein | 2.7.7.48 | 0.444 | |
| 3bug | AEH | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.444 | |
| 2x7h | PFN | Prostaglandin reductase 3 | 1 | 0.443 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1cul | FOK | Adenylate cyclase type 2 | / | 0.442 | |
| 1cul | FOK | Adenylate cyclase type 5 | / | 0.442 | |
| 3d64 | NAD | Adenosylhomocysteinase | / | 0.442 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 1l7x | 700 | Glycogen phosphorylase, liver form | 2.4.1.1 | 0.441 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.441 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.441 | |
| 2fhj | H4Z | Formylmethanofuran--tetrahydromethanopterin formyltransferase | 2.3.1.101 | 0.440 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.440 |