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 |
|---|---|---|---|
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.635 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.614 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.606 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.585 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.571 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.570 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.562 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.557 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.555 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.554 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.544 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.540 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.532 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.529 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.528 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 2v16 | C47 | Renin | 3.4.23.15 | 0.524 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.520 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.520 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.517 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.514 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.513 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.509 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.508 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.506 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.504 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 3vsw | R31 | Renin | 3.4.23.15 | 0.502 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.502 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.501 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.499 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 2i4q | UA4 | Renin | 3.4.23.15 | 0.497 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 3vg1 | 0GT | Beta-secretase 1 | 3.4.23.46 | 0.496 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.495 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.494 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.494 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.493 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.492 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.490 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.489 | |
| 4dh6 | 0KN | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.485 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.484 | |
| 3vyd | VYD | Renin | 3.4.23.15 | 0.484 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.483 | |
| 2g21 | L1B | Renin | 3.4.23.15 | 0.483 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.483 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.482 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.481 | |
| 4b77 | 54M | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 0.481 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.480 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.479 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.478 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.476 | |
| 3zkn | WZV | Beta-secretase 2 | 3.4.23.45 | 0.475 | |
| 4g7g | VFV | Lanosterol 14-alpha-demethylase | / | 0.474 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.473 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.471 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.467 | |
| 3vyf | VYF | Renin | 3.4.23.15 | 0.467 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 | 0.466 | |
| 1psa | 0ZL | Pepsin A | 3.4.23.1 | 0.465 | |
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 | 0.465 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.464 | |
| 5ein | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.464 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.461 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 1bim | 0QB | Renin | 3.4.23.15 | 0.460 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.458 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4zow | CLM | Multidrug transporter MdfA | / | 0.458 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.457 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 1h5q | NAP | NADP-dependent mannitol dehydrogenase | 1.1.1.138 | 0.455 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 5eio | NAP | [LysW]-L-2-aminoadipate 6-phosphate reductase | / | 0.452 | |
| 1bvr | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.451 | |
| 1t2c | NAI | L-lactate dehydrogenase | 1.1.1.27 | 0.451 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.451 | |
| 2oap | ANP | Type II secretion system protein (GspE-2) | / | 0.451 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.451 | |
| 3udk | 095 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4xj4 | 3AT | Cyclic GMP-AMP synthase | / | 0.451 | |
| 2dft | ADP | Shikimate kinase | 2.7.1.71 | 0.450 | |
| 4e2x | TYD | Methyltransferase | / | 0.450 | |
| 4gdy | 0X1 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.450 | |
| 1h73 | ANP | Homoserine kinase | 2.7.1.39 | 0.449 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4ejm | NAP | Putative zinc-binding dehydrogenase | / | 0.449 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.448 | |
| 4nbw | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.448 | |
| 4uwm | FMN | 3,6-diketocamphane 1,6 monooxygenase | 1.14.13 | 0.448 | |
| 2b37 | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.447 | |
| 4lxj | LAN | Lanosterol 14-alpha demethylase | 1.14.13.70 | 0.447 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.445 | |
| 3iqi | ASN_GLU_ASN_ILE | Cysteine synthase | 2.5.1.47 | 0.445 | |
| 1b5e | DCM | Deoxycytidylate 5-hydroxymethyltransferase | 2.1.2.8 | 0.444 | |
| 3b70 | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.444 | |
| 3qls | NDP | Dihydrofolate reductase | 1.5.1.3 | 0.444 | |
| 1qrp | HH0 | Pepsin A-4 | 3.4.23.1 | 0.443 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.443 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.443 | |
| 3lqf | NAD | Galactitol dehydrogenase | / | 0.443 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.442 | |
| 2g26 | 3LG | Renin | 3.4.23.15 | 0.442 | |
| 3f03 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 3psy | RB9 | Endothiapepsin | 3.4.23.22 | 0.442 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.441 | |
| 4eyw | L0R | Carnitine O-palmitoyltransferase 2, mitochondrial | 2.3.1.21 | 0.441 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.441 | |
| 1g6k | NAD | Glucose 1-dehydrogenase | 1.1.1.47 | 0.440 | |
| 2vn1 | FK5 | Peptidylprolyl isomerase | / | 0.440 | |
| 2wat | COA | Fatty acid synthase subunit alpha | 2.3.1.86 | 0.440 |