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 |
|---|---|---|---|
| 3n4l | 842 | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 3n4l | 842 | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 0.619 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.592 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.551 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.530 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.521 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.513 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 4ewo | 996 | Beta-secretase 1 | 3.4.23.46 | 0.510 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.502 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 3udn | 09B | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 3vf3 | 0GS | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.494 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.487 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.480 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.480 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.480 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.473 | |
| 1ra8 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3oaf | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.473 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1dhf | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.470 | |
| 1u71 | MXA | Dihydrofolate reductase | 1.5.1.3 | 0.469 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 1jg0 | DDT | Thymidylate synthase | / | 0.466 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.464 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.464 | |
| 2a0w | DIH | Purine nucleoside phosphorylase | 2.4.2.1 | 0.463 | |
| 1rd7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 1s3u | TQD | Dihydrofolate reductase | 1.5.1.3 | 0.462 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 3n0h | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.461 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.460 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 1e2n | RCA | Thymidine kinase | / | 0.458 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.458 | |
| 4g95 | OAG | Dihydrofolate reductase | 1.5.1.3 | 0.458 | |
| 4k9o | TPP | Benzoylformate decarboxylase | 4.1.1.7 | 0.458 | |
| 1ra3 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.457 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.456 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 5e5h | 0T1 | Succinyl-CoA:acetate CoA-transferase | / | 0.455 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.454 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.454 | |
| 1re7 | FOL | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4i1i | NAD | Malate dehydrogenase | / | 0.453 | |
| 4m6j | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.453 | |
| 4rlh | 0WE | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.453 | |
| 2dhf | DZF | Dihydrofolate reductase | 1.5.1.3 | 0.452 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.452 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.452 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 1diu | BDM | Dihydrofolate reductase | 1.5.1.3 | 0.451 | |
| 2he5 | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.451 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE26 | / | 0.451 | |
| 4x28 | FDA | Acyl-CoA dehydrogenase FadE27 | / | 0.451 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.450 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.450 | |
| 2vwq | NAP | Glucose 1-dehydrogenase | / | 0.450 | |
| 3zei | AWH | O-acetylserine sulfhydrylase | / | 0.450 | |
| 4a8v | 2AN | Major pollen allergen Bet v 1-J | / | 0.450 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.450 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.449 | |
| 2c20 | NAD | UDP-glucose 4-epimerase | / | 0.449 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.449 | |
| 3otw | COA | Phosphopantetheine adenylyltransferase | / | 0.449 | |
| 4bfw | ZVW | Pantothenate kinase | 2.7.1.33 | 0.448 | |
| 1ddr | MTX | Dihydrofolate reductase | 1.5.1.3 | 0.447 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.447 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.447 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.447 | |
| 4j1t | NAP | NAD(P) transhydrogenase subunit beta | / | 0.447 | |
| 1dr3 | TAP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.446 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.446 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 4b4v | L34 | Bifunctional protein FolD | / | 0.446 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4pgh | SAM | Caffeic acid O-methyltransferase | / | 0.445 | |
| 1e5q | NDP | Saccharopine dehydrogenase [NADP(+), L-glutamate-forming] | 1.5.1.10 | 0.444 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.444 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.444 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.443 | |
| 1lbc | CYZ | Glutamate receptor 2 | / | 0.443 | |
| 1s20 | NAD | 2,3-diketo-L-gulonate reductase | 1.1.1.130 | 0.443 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.443 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.443 | |
| 3nf4 | FAD | Acyl-CoA dehydrogenase domain-containing protein | / | 0.443 | |
| 3s3v | TOP | Dihydrofolate reductase | 1.5.1.3 | 0.443 | |
| 3to3 | ATP | Petrobactin biosynthesis protein AsbB | / | 0.443 | |
| 1rx8 | NAP | Dihydrofolate reductase | 1.5.1.3 | 0.442 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.442 | |
| 3bts | NAD | Galactose/lactose metabolism regulatory protein GAL80 | / | 0.442 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.442 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.442 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.442 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.442 | |
| 4fmx | CNL | 1,8-cineole 2-endo-monooxygenase | 1.14.13.156 | 0.442 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.441 | |
| 2yxu | ATP | Pyridoxal kinase | 2.7.1.35 | 0.441 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4dus | 0MP | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 1jdt | MTA | Purine nucleoside phosphorylase | / | 0.440 | |
| 1n2s | NAI | dTDP-4-dehydrorhamnose reductase | 1.1.1.133 | 0.440 | |
| 1r6u | TYM | Tryptophan--tRNA ligase, cytoplasmic | 6.1.1.2 | 0.440 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.440 | |
| 4bge | PYW | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.440 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.440 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.440 |