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 Modes are compared using Grim.
For more information, please see the following publication:
Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Mode Similarity |
Align |
|---|---|---|---|---|---|
| 2fdp | FRP | Beta-secretase 1 | 3.4.23.46 | 1.380 | |
| 3k5f | AYH | Beta-secretase 1 | 3.4.23.46 | 1.016 | |
| 3k5g | BJC | Beta-secretase 1 | 3.4.23.46 | 0.827 | |
| 2f3f | AXF | Beta-secretase 1 | 3.4.23.46 | 0.820 | |
| 3k5d | XLI | Beta-secretase 1 | 3.4.23.46 | 0.818 | |
| 2g94 | ZPQ | Beta-secretase 1 | 3.4.23.46 | 0.813 | |
| 2wf2 | ZY2 | Beta-secretase 1 | 3.4.23.46 | 0.813 | |
| 3cid | 318 | Beta-secretase 1 | 3.4.23.46 | 0.813 | |
| 2oah | QIN | Beta-secretase 1 | 3.4.23.46 | 0.811 | |
| 2vie | VG0 | Beta-secretase 1 | 3.4.23.46 | 0.807 | |
| 3dv1 | AR9 | Beta-secretase 1 | 3.4.23.46 | 0.806 | |
| 2vnm | CM8 | Beta-secretase 1 | 3.4.23.46 | 0.800 | |
| 2p83 | MR0 | Beta-secretase 1 | 3.4.23.46 | 0.797 | |
| 3dm6 | 757 | Beta-secretase 1 | 3.4.23.46 | 0.789 | |
| 2hiz | LIJ | Beta-secretase 1 | 3.4.23.46 | 0.786 | |
| 2xfi | XFI | Beta-secretase 1 | 3.4.23.46 | 0.786 | |
| 2xfk | AA9 | Beta-secretase 1 | 3.4.23.46 | 0.784 | |
| 2wez | ZYE | Beta-secretase 1 | 3.4.23.46 | 0.783 | |
| 3cib | 314 | Beta-secretase 1 | 3.4.23.46 | 0.782 | |
| 3lpk | Z76 | Beta-secretase 1 | 3.4.23.46 | 0.782 | |
| 3duy | AFJ | Beta-secretase 1 | 3.4.23.46 | 0.779 | |
| 3veu | 0GO | Beta-secretase 1 | 3.4.23.46 | 0.777 | |
| 3nsh | 957 | Beta-secretase 1 | 3.4.23.46 | 0.776 | |
| 4i0i | 957 | Beta-secretase 1 | 3.4.23.46 | 0.776 | |
| 2viy | VG3 | Beta-secretase 1 | 3.4.23.46 | 0.773 | |
| 1w51 | L01 | Beta-secretase 1 | 3.4.23.46 | 0.770 | |
| 2p4j | 23I | Beta-secretase 1 | 3.4.23.46 | 0.769 | |
| 3dv5 | BAV | Beta-secretase 1 | 3.4.23.46 | 0.765 | |
| 2wf3 | ZY3 | Beta-secretase 1 | 3.4.23.46 | 0.764 | |
| 2f3e | AXQ | Beta-secretase 1 | 3.4.23.46 | 0.763 | |
| 3r2f | PB0 | Beta-secretase 1 | 3.4.23.46 | 0.760 | |
| 4y38 | 0A9 | Endothiapepsin | 3.4.23.22 | 0.760 | |
| 2viz | VG4 | Beta-secretase 1 | 3.4.23.46 | 0.755 | |
| 3ixj | 586 | Beta-secretase 1 | 3.4.23.46 | 0.753 | |
| 4dpf | 0LG | Beta-secretase 1 | 3.4.23.46 | 0.750 | |
| 4gid | 0GH | Beta-secretase 1 | 3.4.23.46 | 0.749 | |
| 1bxo | PP7 | Penicillopepsin-1 | 3.4.23.20 | 0.741 | |
| 4k9h | 1QU | Beta-secretase 1 | 3.4.23.46 | 0.740 | |
| 2iqg | F2I | Beta-secretase 1 | 3.4.23.46 | 0.738 | |
| 3ohf | 3HF | Beta-secretase 1 | 3.4.23.46 | 0.738 | |
| 2vij | C44 | Beta-secretase 1 | 3.4.23.46 | 0.736 | |
| 3ixk | 929 | Beta-secretase 1 | 3.4.23.46 | 0.736 | |
| 1bxq | PP8 | Penicillopepsin-1 | 3.4.23.20 | 0.735 | |
| 4dpi | 0N1 | Beta-secretase 1 | 3.4.23.46 | 0.734 | |
| 4fco | 0U4 | Beta-secretase 1 | 3.4.23.46 | 0.732 | |
| 3k5c | 0BI | Beta-secretase 1 | 3.4.23.46 | 0.729 | |
| 1eag | A70 | Candidapepsin-2 | 3.4.23.24 | 0.719 | |
| 3pww | ROC | Endothiapepsin | 3.4.23.22 | 0.717 | |
| 2b8v | 3BN | Beta-secretase 1 | 3.4.23.46 | 0.714 | |
| 2wf0 | ZY0 | Beta-secretase 1 | 3.4.23.46 | 0.712 | |
| 1gvv | 0GM | Endothiapepsin | 3.4.23.22 | 0.711 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.706 | |
| 3i25 | MV7 | Beta-secretase 1 | 3.4.23.46 | 0.703 | |
| 3ohh | 3HH | Beta-secretase 1 | 3.4.23.46 | 0.701 | |
| 2p8h | MY9 | Beta-secretase 1 | 3.4.23.46 | 0.698 | |
| 4ke0 | 1R8 | Beta-secretase 1 | 3.4.23.46 | 0.698 | |
| 2hm1 | LIQ | Beta-secretase 1 | 3.4.23.46 | 0.696 | |
| 1w6h | TIT | Plasmepsin-2 | 3.4.23.39 | 0.694 | |
| 2b8l | 5HA | Beta-secretase 1 | 3.4.23.46 | 0.691 | |
| 1gvw | 0EM | Endothiapepsin | 3.4.23.22 | 0.688 | |
| 2qzl | IXS | Beta-secretase 1 | 3.4.23.46 | 0.686 | |
| 4ke1 | 1R6 | Beta-secretase 1 | 3.4.23.46 | 0.686 | |
| 3own | 3OX | Renin | 3.4.23.15 | 0.683 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.683 | |
| 2jji | 0QS | Endothiapepsin | 3.4.23.22 | 0.681 | |
| 2vj7 | VG6 | Beta-secretase 1 | 3.4.23.46 | 0.681 | |
| 2vkm | BSD | Beta-secretase 1 | 3.4.23.46 | 0.680 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.680 | |
| 2wf4 | ZY4 | Beta-secretase 1 | 3.4.23.46 | 0.676 | |
| 3dcr | KVS | Protease | / | 0.676 | |
| 3vye | VYE | Renin | 3.4.23.15 | 0.676 | |
| 2vnn | CM7 | Beta-secretase 1 | 3.4.23.46 | 0.675 | |
| 2vj6 | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.674 | |
| 4lxa | 1YS | Beta-secretase 1 | 3.4.23.46 | 0.672 | |
| 3lpi | Z74 | Beta-secretase 1 | 3.4.23.46 | 0.671 | |
| 1bil | 0IU | Renin | 3.4.23.15 | 0.670 | |
| 3pi5 | 3P5 | Beta-secretase 1 | 3.4.23.46 | 0.669 | |
| 1mtr | PI6 | Gag-Pol polyprotein | 3.4.23.16 | 0.668 | |
| 1xe5 | 5FE | Plasmepsin-2 | 3.4.23.39 | 0.665 | |
| 3lpj | Z75 | Beta-secretase 1 | 3.4.23.46 | 0.665 | |
| 2xfj | VG5 | Beta-secretase 1 | 3.4.23.46 | 0.663 | |
| 1npv | L27 | Gag-Pol polyprotein | 3.4.23.16 | 0.660 | |
| 4j55 | 031 | Gag-Pol polyprotein | 3.4.23.16 | 0.659 | |
| 3nxe | 2NC | Protease | / | 0.658 | |
| 3skg | PB8 | Beta-secretase 1 | 3.4.23.46 | 0.657 | |
| 2ph6 | 712 | Beta-secretase 1 | 3.4.23.46 | 0.656 | |
| 3vuc | HHE | Renin | 3.4.23.15 | 0.656 | |
| 3cic | 316 | Beta-secretase 1 | 3.4.23.46 | 0.654 | |
| 3hzc | 2NC | Protease | / | 0.654 | |
| 3qbh | QBH | Beta-secretase 1 | 3.4.23.46 | 0.654 | |
| 2ph8 | 35A | Beta-secretase 1 | 3.4.23.46 | 0.653 | |
| 3qpj | N4I | Gag-Pol polyprotein | 3.4.23.16 | 0.653 | |
| 1zap | A70 | Candidapepsin-2 | 3.4.23.24 | 0.651 |