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 |
|---|---|---|---|
| 3pll | F06 | Endothiapepsin | 3.4.23.22 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3pll | F06 | Endothiapepsin | 3.4.23.22 | 1.000 | |
| 4y3r | F06 | Endothiapepsin | 3.4.23.22 | 0.757 | |
| 3pld | F90 | Endothiapepsin | 3.4.23.22 | 0.701 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.690 | |
| 3prs | RIT | Endothiapepsin | 3.4.23.22 | 0.643 | |
| 1e81 | M91 | Endothiapepsin | 3.4.23.22 | 0.619 | |
| 3pmy | 41L | Endothiapepsin | 3.4.23.22 | 0.617 | |
| 1od1 | 0QS | Endothiapepsin | 3.4.23.22 | 0.616 | |
| 3pgi | F41 | Endothiapepsin | 3.4.23.22 | 0.613 | |
| 4y38 | 0A9 | Endothiapepsin | 3.4.23.22 | 0.611 | |
| 3t6i | NC8 | Endothiapepsin | 3.4.23.22 | 0.608 | |
| 3pww | ROC | Endothiapepsin | 3.4.23.22 | 0.593 | |
| 3pm4 | F5N | Endothiapepsin | 3.4.23.22 | 0.589 | |
| 1e82 | M90 | Endothiapepsin | 3.4.23.22 | 0.588 | |
| 4y3z | F41 | Endothiapepsin | 3.4.23.22 | 0.588 | |
| 1gvt | 2ZS | Endothiapepsin | 3.4.23.22 | 0.586 | |
| 2jji | 0QS | Endothiapepsin | 3.4.23.22 | 0.584 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.584 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.582 | |
| 4yd7 | F5N | Endothiapepsin | 3.4.23.22 | 0.581 | |
| 3t7p | 7SP | Endothiapepsin | 3.4.23.22 | 0.579 | |
| 1gvw | 0EM | Endothiapepsin | 3.4.23.22 | 0.578 | |
| 3t7x | 4SH | Endothiapepsin | 3.4.23.22 | 0.574 | |
| 2v00 | V15 | Endothiapepsin | 3.4.23.22 | 0.573 | |
| 2jjj | 0QS | Endothiapepsin | 3.4.23.22 | 0.571 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.567 | |
| 1ppk | IVV | Penicillopepsin-1 | 3.4.23.20 | 0.546 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.541 | |
| 1ppm | 0P1 | Penicillopepsin-1 | 3.4.23.20 | 0.539 | |
| 4zea | IMI | Endothiapepsin | 3.4.23.22 | 0.532 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.531 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.519 | |
| 2web | PP4 | Penicillopepsin-1 | 3.4.23.20 | 0.510 | |
| 2wec | PP5 | Penicillopepsin-1 | 3.4.23.20 | 0.509 | |
| 1e80 | 0GQ | Endothiapepsin | 3.4.23.22 | 0.508 | |
| 1zap | A70 | Candidapepsin-2 | 3.4.23.24 | 0.508 | |
| 2wed | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.507 | |
| 3tne | RIT | Candidapepsin-1 | 3.4.23.24 | 0.507 | |
| 3pbz | F02 | Endothiapepsin | 3.4.23.22 | 0.504 | |
| 1eag | A70 | Candidapepsin-2 | 3.4.23.24 | 0.501 | |
| 1lf3 | EH5 | Plasmepsin-2 | 3.4.23.39 | 0.501 | |
| 1bxq | PP8 | Penicillopepsin-1 | 3.4.23.20 | 0.493 | |
| 3q70 | RIT | Candidapepsin-2 | 3.4.23.24 | 0.493 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.491 | |
| 3lit | E15 | Protease | / | 0.485 | |
| 1ppl | 1Z7 | Penicillopepsin-1 | 3.4.23.20 | 0.484 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.483 | |
| 2wea | PP6 | Penicillopepsin-1 | 3.4.23.20 | 0.483 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 3r7k | FDA | Probable acyl CoA dehydrogenase | / | 0.479 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.476 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.475 | |
| 4exg | 916 | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.474 | |
| 1gqt | ACP | Ribokinase | / | 0.472 | |
| 4jq7 | KJQ | Epidermal growth factor receptor | 2.7.10.1 | 0.471 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.469 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.466 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.466 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.466 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.465 | |
| 2fxd | DR7 | Pol polyprotein | / | 0.463 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.462 | |
| 1siq | FAD | Glutaryl-CoA dehydrogenase, mitochondrial | 1.3.8.6 | 0.461 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.460 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.460 | |
| 2fm5 | M99 | cAMP-specific 3',5'-cyclic phosphodiesterase 4D | 3.1.4.53 | 0.459 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.459 | |
| 4anx | 534 | Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform | 2.7.1.153 | 0.459 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 3g5s | FAD | Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO | / | 0.458 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.457 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 1ege | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.456 | |
| 1nuu | NAD | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.456 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4y3q | F02 | Endothiapepsin | 3.4.23.22 | 0.456 | |
| 2nru | T12 | Interleukin-1 receptor-associated kinase 4 | 2.7.11.1 | 0.455 | |
| 2qnq | QN3 | Gag-Pol polyprotein | 3.4.23.16 | 0.455 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4b72 | 2FB | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 1udy | FAD | Medium-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.7 | 0.454 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.454 | |
| 3wsj | MK1 | Protease | / | 0.454 | |
| 4k8s | 1QT | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 5jsc | FAD | Putative acyl-CoA dehydrogenase | / | 0.454 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.453 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.453 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.452 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3sf6 | FDA | Glutaryl-CoA dehydrogenase | / | 0.452 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.451 | |
| 2vtb | FAD | Cryptochrome DASH, chloroplastic/mitochondrial | / | 0.451 | |
| 3s1d | ZIR | Cytokinin dehydrogenase 1 | 1.5.99.12 | 0.451 | |
| 4zj8 | SUV | Orexin receptor type 1 | / | 0.451 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.450 | |
| 2g22 | 6IG | Renin | 3.4.23.15 | 0.450 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4a81 | DXC | Major pollen allergen Bet v 1-A | / | 0.450 | |
| 1ib0 | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.449 | |
| 1vik | BAY | Gag-Pol polyprotein | / | 0.449 | |
| 2vig | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | 1.3.8.1 | 0.449 | |
| 3vsx | R32 | Renin | 3.4.23.15 | 0.449 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.449 | |
| 4z64 | ILE_THR_GLN_TYS_TYS | Phytosulfokine receptor 1 | 2.7.11.1 | 0.449 | |
| 3k1w | BFX | Renin | 3.4.23.15 | 0.448 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.448 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 2po7 | CHD | Ferrochelatase, mitochondrial | 4.99.1.1 | 0.447 | |
| 1nuq | NXX | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.446 | |
| 1yre | COA | Uncharacterized protein | / | 0.446 | |
| 2d1y | NAD | Oxidoreductase, short-chain dehydrogenase/reductase family | / | 0.446 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2ii6 | C5P | Alpha-2,3/2,6-sialyltransferase/sialidase | / | 0.446 | |
| 3rtn | RTN | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4c34 | STU | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.446 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3liv | E16 | Protease | / | 0.445 | |
| 4j5j | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.445 | |
| 1msn | JE2 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 2el0 | SAH | Diphthine synthase | / | 0.444 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 3oxv | 478 | Gag-Pol polyprotein | 3.4.23.16 | 0.444 | |
| 3uic | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | / | 0.444 | |
| 4hy6 | FJ1 | Heat shock protein HSP 90-alpha | / | 0.444 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4l7j | 1W2 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 5ifi | PRX | Acetyl-coenzyme A synthetase | / | 0.444 | |
| 1zth | ADP | RIO-type serine/threonine-protein kinase Rio1 | 2.7.11.1 | 0.443 | |
| 3clr | FAD | Electron transfer flavoprotein subunit alpha | / | 0.443 | |
| 3liq | E14 | Protease | / | 0.443 | |
| 3t6i | NC9 | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 4i8v | BHF | Cytochrome P450 1A1 | 1.14.14.1 | 0.443 | |
| 4ipw | 1G7 | Mycocyclosin synthase | 1.14.21.9 | 0.443 | |
| 4ocp | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.443 | |
| 5f8e | SAH | Possible transcriptional regulatory protein | / | 0.443 | |
| 4s0v | SUV | Orexin receptor type 2 | / | 0.443 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.442 | |
| 3el9 | DR7 | Gag-Pol polyprotein | 3.4.23.16 | 0.442 | |
| 4ocv | ANP | Aminoglycoside phosphotransferase | / | 0.442 | |
| 1gg5 | E09 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.441 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4aos | FAD | Steroid monooxygenase | / | 0.441 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.441 | |
| 4iae | 1DX | Alr2278 protein | / | 0.441 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.440 | |
| 1mrw | K57 | Gag-Pol polyprotein | 3.4.23.16 | 0.440 | |
| 1n2i | PAJ | Pantothenate synthetase | 6.3.2.1 | 0.440 | |
| 1u8v | FAD | 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA-Delta-isomerase | / | 0.440 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.440 | |
| 3toh | 079 | Gag-Pol polyprotein | 2.7.7.49 | 0.440 | |
| 4bgg | 844 | Activin receptor type-1 | 2.7.11.30 | 0.440 | |
| 4gl4 | NAI | Alcohol dehydrogenase class-3 | / | 0.440 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4xr9 | NAD | CalS8 | / | 0.440 |