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 |
|---|---|---|---|
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3qow | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 1.000 | |
| 1nw3 | SAM | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.636 | |
| 3sr4 | TT8 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.631 | |
| 4eki | 0QK | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.512 | |
| 4ekg | 0QJ | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.508 | |
| 4obw | SAM | 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial | / | 0.476 | |
| 2eg5 | SAH | 7-methylxanthosine synthase 1 | / | 0.475 | |
| 2fgk | ATP | Alpha-hemolysin translocation ATP-binding protein HlyB | / | 0.463 | |
| 2zjm | F1M | Beta-secretase 1 | 3.4.23.46 | 0.463 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.461 | |
| 5jr3 | SAH | Carminomycin 4-O-methyltransferase DnrK | 2.1.1.292 | 0.459 | |
| 3q87 | SAM | N6 ADENINE SPECIFIC DNA METHYLASE (METHYLTRANSFERASE SUPERFAMILY) | / | 0.458 | |
| 1nw5 | SAM | Modification methylase RsrI | 2.1.1.72 | 0.457 | |
| 4ek9 | EP4 | Histone-lysine N-methyltransferase, H3 lysine-79 specific | 2.1.1.43 | 0.457 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.456 | |
| 4rtr | SAM | DNA adenine methylase | 2.1.1.72 | 0.454 | |
| 2gci | MRR | Probable alpha-methylacyl-CoA racemase Mcr (2-methylacyl-CoA racemase) (2-arylpropionyl-CoA epimerase ) | / | 0.453 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.450 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.449 | |
| 1wy7 | SAH | Uncharacterized protein | / | 0.449 | |
| 2hv9 | SFG | mRNA cap guanine-N7 methyltransferase | 2.1.1.56 | 0.449 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.448 | |
| 5bp9 | SAH | Putative methyltransferase protein | / | 0.448 | |
| 3a25 | SAM | tRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase | / | 0.447 | |
| 3pt9 | SAH | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.447 | |
| 6cts | CIC | Citrate synthase, mitochondrial | 2.3.3.1 | 0.447 | |
| 3ldf | SAH | Uncharacterized protein | / | 0.446 | |
| 4ap7 | F47 | Hepatocyte growth factor receptor | 2.7.10.1 | 0.445 | |
| 2ewp | TXF | Estrogen-related receptor gamma | / | 0.443 | |
| 3gw9 | VNI | Lanosterol 14-alpha-demethylase | / | 0.443 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 4frj | DWB | Beta-secretase 1 | 3.4.23.46 | 0.443 | |
| 1fwm | CB3 | Thymidylate synthase | / | 0.442 | |
| 1jqi | FAD | Short-chain specific acyl-CoA dehydrogenase, mitochondrial | / | 0.442 | |
| 3swr | SFG | DNA (cytosine-5)-methyltransferase 1 | 2.1.1.37 | 0.442 | |
| 1boo | SAH | Modification methylase PvuII | 2.1.1.113 | 0.441 | |
| 3vqs | JT1 | Genome polyprotein | / | 0.441 | |
| 4b05 | 32D | Beta-secretase 1 | 3.4.23.46 | 0.441 | |
| 2bf4 | FMN | NADPH--cytochrome P450 reductase | / | 0.440 | |
| 4acx | S8Z | Beta-secretase 1 | 3.4.23.46 | 0.440 |