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 |
|---|---|---|---|
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 1.000 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.676 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.644 | |
| 1tqf | 32P | Beta-secretase 1 | 3.4.23.46 | 0.627 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.627 | |
| 2is0 | I03 | Beta-secretase 1 | 3.4.23.46 | 0.622 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.605 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.593 | |
| 2irz | I02 | Beta-secretase 1 | 3.4.23.46 | 0.582 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.552 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.545 | |
| 2ntr | L00 | Beta-secretase 1 | 3.4.23.46 | 0.523 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.522 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.521 | |
| 4djy | 0KR | Beta-secretase 1 | 3.4.23.46 | 0.519 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.512 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.503 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.500 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.488 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.487 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 0.486 | |
| 4h3j | 10W | Beta-secretase 1 | 3.4.23.46 | 0.485 | |
| 2vj9 | VG7 | Beta-secretase 1 | 3.4.23.46 | 0.484 | |
| 4du8 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.482 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.479 | |
| 1me6 | IVS | Plasmepsin-2 | 3.4.23.39 | 0.477 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.476 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.472 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 4h3f | 10O | Beta-secretase 1 | 3.4.23.46 | 0.471 | |
| 1rne | C60 | Renin | 3.4.23.15 | 0.467 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.467 | |
| 2cf6 | NAP | Cinnamyl alcohol dehydrogenase 5 | 1.1.1.195 | 0.465 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2il2 | LIX | Renin | 3.4.23.15 | 0.463 | |
| 1ndh | FAD | NADH-cytochrome b5 reductase 3 | 1.6.2.2 | 0.461 | |
| 1x1b | SAH | C-20 methyltransferase | / | 0.459 | |
| 3n4l | 842 | Beta-secretase 1 | 3.4.23.46 | 0.459 | |
| 2qs3 | UBE | Glutamate receptor ionotropic, kainate 1 | / | 0.458 | |
| 2wns | OMP | Uridine 5'-monophosphate synthase | 2.4.2.10 | 0.458 | |
| 4i0j | 842 | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 2xy3 | DUP | SPBc2 prophage-derived deoxyuridine 5'-triphosphate nucleotidohydrolase YosS | 3.6.1.23 | 0.457 | |
| 4m83 | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.456 | |
| 1xe6 | 5FP | Plasmepsin-2 | 3.4.23.39 | 0.455 | |
| 2e15 | SAH | Diphthine synthase | / | 0.453 | |
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.453 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.453 | |
| 4b70 | WM9 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3qi1 | C6A | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3djj | FAD | Glutathione reductase, mitochondrial | 1.8.1.7 | 0.451 | |
| 4epl | JAI | Jasmonic acid-amido synthetase JAR1 | 6.3.2 | 0.451 | |
| 1x1d | SAH | C-20 methyltransferase | / | 0.449 | |
| 2c9z | QUE | Anthocyanidin 3-O-glucosyltransferase 2 | 2.4.1.115 | 0.449 | |
| 2f3r | G5P | Guanylate kinase | 2.7.4.8 | 0.449 | |
| 4bfz | ZVZ | Pantothenate kinase | 2.7.1.33 | 0.449 | |
| 1o9b | NAI | Quinate/shikimate dehydrogenase | / | 0.448 | |
| 4fdu | IHS | Putative multiple inositol polyphosphate histidine phosphatase 1 | / | 0.448 | |
| 4nbt | NAD | 3-oxoacyl-[acyl-carrier-protein] reductase | / | 0.448 | |
| 1d4a | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.447 | |
| 1nvt | NAP | Shikimate dehydrogenase (NADP(+)) | / | 0.447 | |
| 2a9y | 26A | Adenosine kinase | 2.7.1.20 | 0.447 | |
| 2hfu | MEV | Mevalonate kinase | / | 0.447 | |
| 2g1n | 1IG | Renin | 3.4.23.15 | 0.446 | |
| 3dga | NDP | Bifunctional dihydrofolate reductase-thymidylate synthase | 1.5.1.3 | 0.446 | |
| 3te5 | NAI | 5'-AMP-activated protein kinase subunit gamma | / | 0.446 | |
| 3w8e | NAD | 3-hydroxybutyrate dehydrogenase | / | 0.446 | |
| 4frs | 0V6 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.445 | |
| 1g1a | NAD | dTDP-glucose 4,6-dehydratase | / | 0.445 | |
| 2iyf | ERY | Oleandomycin glycosyltransferase | 2.4.1 | 0.445 | |
| 4dx7 | DM2 | Multidrug efflux pump subunit AcrB | / | 0.445 | |
| 4y35 | F90 | Endothiapepsin | 3.4.23.22 | 0.445 | |
| 1uda | UFG | UDP-glucose 4-epimerase | 5.1.3.2 | 0.444 | |
| 2i3g | NAP | N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | 0.444 | |
| 3gqv | NAP | Enoyl reductase LovC | 1 | 0.444 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 4k6f | NAP | Putative Acetoacetyl-CoA reductase | / | 0.444 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.443 | |
| 2f7x | 4EA | cAMP-dependent protein kinase catalytic subunit alpha | 2.7.11.11 | 0.443 | |
| 4y3j | HIC | Endothiapepsin | 3.4.23.22 | 0.443 | |
| 1a72 | PAD | Alcohol dehydrogenase E chain | 1.1.1.1 | 0.442 | |
| 1hdc | CBO | 3-alpha-(or 20-beta)-hydroxysteroid dehydrogenase | 1.1.1.53 | 0.442 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.442 | |
| 3c1y | 2BA | DNA integrity scanning protein DisA | / | 0.441 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 3tjz | GNP | ADP-ribosylation factor 1 | / | 0.440 |