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 |
|---|---|---|---|
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4i0z | 1BB | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 4i1c | 1BE | Beta-secretase 1 | 3.4.23.46 | 0.642 | |
| 4i10 | 1BS | Beta-secretase 1 | 3.4.23.46 | 0.614 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.566 | |
| 3exo | 5MS | Beta-secretase 1 | 3.4.23.46 | 0.554 | |
| 3tpr | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.544 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.543 | |
| 4j0y | 1H6 | Beta-secretase 1 | 3.4.23.46 | 0.542 | |
| 4lc7 | 1WP | Beta-secretase 1 | 3.4.23.46 | 0.533 | |
| 4jpe | 1M7 | Beta-secretase 1 | 3.4.23.46 | 0.527 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.525 | |
| 3zmg | 6Z0 | Beta-secretase 1 | 3.4.23.46 | 0.524 | |
| 4j1c | 1HO | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 4i0f | 1BF | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 4b78 | KGG | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 4j1k | 1HG | Beta-secretase 1 | 3.4.23.46 | 0.518 | |
| 4j17 | 1HQ | Beta-secretase 1 | 3.4.23.46 | 0.516 | |
| 4ha5 | 13W | Beta-secretase 1 | 3.4.23.46 | 0.513 | |
| 2va7 | C27 | Beta-secretase 1 | 3.4.23.46 | 0.511 | |
| 3zks | WZV | Beta-secretase 2 | 3.4.23.45 | 0.511 | |
| 4h3g | 10Q | Beta-secretase 1 | 3.4.23.46 | 0.507 | |
| 4fs4 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 4i0h | 1BL | Beta-secretase 1 | 3.4.23.46 | 0.505 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.504 | |
| 4i11 | 1CH | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 4l7g | 1W0 | Beta-secretase 1 | 3.4.23.46 | 0.498 | |
| 4azy | 7F3 | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 4j0p | 1H8 | Beta-secretase 1 | 3.4.23.46 | 0.497 | |
| 4djw | 0KP | Beta-secretase 1 | 3.4.23.46 | 0.493 | |
| 3zki | WZV | Beta-secretase 2 | 3.4.23.45 | 0.491 | |
| 4b1c | 1B1 | Beta-secretase 1 | 3.4.23.46 | 0.491 | |
| 2ohp | 6IP | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 2ohr | 8IP | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 4j1e | 1HM | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 1i5r | HYC | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.485 | |
| 4jpc | 1M6 | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 3zlq | 6T9 | Beta-secretase 2 | 3.4.23.45 | 0.484 | |
| 4fm8 | 0UQ | Beta-secretase 1 | 3.4.23.46 | 0.480 | |
| 4djx | 0KQ | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4lxm | 1YU | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.477 | |
| 3kmy | D8Y | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 4h1e | 10J | Beta-secretase 1 | 3.4.23.46 | 0.475 | |
| 2ohq | 7IP | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 4dju | 0KK | Beta-secretase 1 | 3.4.23.46 | 0.474 | |
| 4mrm | 2BY | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.473 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.470 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.470 | |
| 3h0b | B35 | Beta-secretase 1 | 3.4.23.46 | 0.469 | |
| 1jmi | UMP | Thymidylate synthase | / | 0.465 | |
| 4trn | NAD | Enoyl-[acyl-carrier-protein] reductase [NADH] | 1.3.1.9 | 0.463 | |
| 4djv | 0KM | Beta-secretase 1 | 3.4.23.46 | 0.460 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.457 | |
| 4bfd | 8T3 | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.456 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4q0k | GA3 | Phytohormone-binding protein | / | 0.456 | |
| 2q15 | 3MR | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 3gwf | NAP | Cyclohexanone monooxygenase | / | 0.455 | |
| 4fse | 0VA | Beta-secretase 1 | 3.4.23.46 | 0.455 | |
| 4yfy | 1YJ | VioF | / | 0.455 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.454 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.453 | |
| 4eag | ATP | 5'-AMP-activated protein kinase subunit gamma-1 | / | 0.453 | |
| 4gdc | NDP | UDP-galactopyranose mutase | / | 0.453 | |
| 1cnf | FAD | Nitrate reductase [NADH] | 1.7.1.1 | 0.452 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.452 | |
| 3kmt | SAH | Histone H3K27 methylase | / | 0.452 | |
| 4h3i | 10V | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2g20 | L1A | Renin | 3.4.23.15 | 0.451 | |
| 3c3x | NAP | Eugenol synthase 1 | 1.1.1.318 | 0.450 | |
| 3zov | WZV | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1xs7 | MMI | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 4hzt | 0ZA | Beta-secretase 1 | 3.4.23.46 | 0.449 | |
| 2g1s | 4IG | Renin | 3.4.23.15 | 0.448 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.448 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4asu | ADP | ATP synthase subunit alpha, mitochondrial | / | 0.448 | |
| 1tsx | UMP | Thymidylate synthase | / | 0.447 | |
| 4b00 | I6X | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 4ca6 | 3EF | Angiotensin-converting enzyme | 3.2.1 | 0.447 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.446 | |
| 2va6 | H24 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 3hl0 | NAD | Maleylacetate reductase | / | 0.446 | |
| 4uym | VOR | 14-alpha sterol demethylase Cyp51B | / | 0.446 | |
| 2g1o | 2IG | Renin | 3.4.23.15 | 0.445 | |
| 2yye | APC | Selenide, water dikinase | 2.7.9.3 | 0.445 | |
| 3kmx | G00 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 4ms1 | 381 | Gamma-aminobutyric acid type B receptor subunit 1 | / | 0.445 | |
| 1x1a | SAM | C-20 methyltransferase | / | 0.444 | |
| 2lfo | GCH | Fatty acid-binding protein, liver | / | 0.444 | |
| 3eu5 | GBO | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3jsx | CC2 | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 4b0q | GMF | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4cf6 | CBD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.444 | |
| 1jtv | TES | Estradiol 17-beta-dehydrogenase 1 | 1.1.1.62 | 0.443 | |
| 4acu | QN7 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.443 | |
| 4bfs | ZVS | Pantothenate kinase | 2.7.1.33 | 0.442 | |
| 1lce | TMF | Thymidylate synthase | / | 0.441 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 4eb7 | PLP | Cysteine desulfurase IscS 2 | / | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.440 | |
| 3dga | UMP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.440 | |
| 3ufl | 508 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.440 |