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 |
|---|---|---|---|
| 4h8i | 11W | Glutamate receptor ionotropic, kainate 2 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 4h8i | 11W | Glutamate receptor ionotropic, kainate 2 | / | 1.000 | |
| 2pbw | DOQ | Glutamate receptor ionotropic, kainate 1 | / | 0.510 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.503 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.501 | |
| 2xxv | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.494 | |
| 3c34 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.490 | |
| 3swq | EPU | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.478 | |
| 4j0v | 1H7 | Beta-secretase 1 | 3.4.23.46 | 0.473 | |
| 3irh | DTP | HD domain protein | / | 0.466 | |
| 4bdo | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.466 | |
| 2geu | COK | Pantothenate kinase | 2.7.1.33 | 0.464 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 2rl2 | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.462 | |
| 1uae | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.461 | |
| 4epq | 0RR | Poly(ADP-ribose) glycohydrolase | / | 0.461 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.458 | |
| 4lxk | 1YT | Beta-secretase 1 | 3.4.23.46 | 0.457 | |
| 4kw5 | 1W6 | Decaprenylphosphoryl-beta-D-ribose oxidase | / | 0.456 | |
| 2g8y | NAD | Hydroxycarboxylate dehydrogenase B | / | 0.455 | |
| 3upk | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.455 | |
| 4f3g | KAI | Glutamate receptor 3 | / | 0.455 | |
| 4rvg | TYD | D-mycarose 3-C-methyltransferase | / | 0.455 | |
| 2iko | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 4bek | XK0 | Beta-secretase 1 | 3.4.23.46 | 0.454 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3kfm | KAI | Glutamate receptor 4 | / | 0.453 | |
| 4j1f | 1HL | Beta-secretase 1 | 3.4.23.46 | 0.453 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 3udq | 09E | Beta-secretase 1 | 3.4.23.46 | 0.452 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.451 | |
| 4drj | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.451 | |
| 4drj | RAP | Peptidyl-prolyl cis-trans isomerase FKBP4 | 5.2.1.8 | 0.451 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.450 | |
| 2v5u | FMN | Flavodoxin | / | 0.450 | |
| 3qm4 | PN0 | Cytochrome P450 2D6 | / | 0.450 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.450 | |
| 5dp2 | NAP | CurF | / | 0.450 | |
| 1fap | RAP | Peptidyl-prolyl cis-trans isomerase FKBP1A | 5.2.1.8 | 0.449 | |
| 1fap | RAP | Serine/threonine-protein kinase mTOR | 2.7.11.1 | 0.449 | |
| 4a31 | 2CB | Glycylpeptide N-tetradecanoyltransferase | / | 0.449 | |
| 1q0z | AKA | Aclacinomycin methylesterase RdmC | 3.1.1.95 | 0.448 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.448 | |
| 3vcy | UD1 | UDP-N-acetylglucosamine 1-carboxyvinyltransferase | / | 0.448 | |
| 1amo | FMN | NADPH--cytochrome P450 reductase | / | 0.447 | |
| 1pua | COA | HAT A1 | / | 0.447 | |
| 2nmt | MIM | Glycylpeptide N-tetradecanoyltransferase | 2.3.1.97 | 0.447 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.447 | |
| 3vf6 | 0H6 | Glucokinase | 2.7.1.2 | 0.447 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.446 | |
| 3bv7 | NAP | 3-oxo-5-beta-steroid 4-dehydrogenase | / | 0.446 | |
| 4bdr | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.446 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.446 | |
| 4pl0 | ANP | Microcin-J25 export ATP-binding/permease protein McjD | / | 0.446 | |
| 1w7h | 3IP | Mitogen-activated protein kinase 14 | / | 0.445 | |
| 2v2z | CDM | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.445 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.445 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.444 | |
| 4d89 | BXD | Beta-secretase 1 | 3.4.23.46 | 0.444 | |
| 2xxy | KAI | Glutamate receptor ionotropic, kainate 2 | / | 0.443 | |
| 4frk | DWD | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4j0t | 6T9 | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 3eku | CY9 | Actin-5C | / | 0.442 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 3hv3 | R49 | Mitogen-activated protein kinase 14 | / | 0.441 | |
| 3wqm | B29 | Diterpene synthase | 3.1.7.8 | 0.441 | |
| 4wh2 | ADP | N-acetylhexosamine 1-kinase | 2.7.1.162 | 0.441 | |
| 1fw0 | KAI | Glutamate receptor 2 | / | 0.440 | |
| 2ivn | ANP | tRNA N6-adenosine threonylcarbamoyltransferase | / | 0.440 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.440 | |
| 3fkt | SII | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.440 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.440 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.440 |