sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2013-12-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.410 | 7.560 | 7.440 | 0.190 | 7.820 | 3 |
| Name: | Serine/threonine-protein kinase PAK 1 |
|---|---|
| ID: | PAK1_HUMAN |
| AC: | Q13153 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| B | 3 % |
| B-Factor: | 75.089 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.976 | 1663.875 |
| % Hydrophobic | % Polar |
|---|---|
| 48.07 | 51.93 |
| According to VolSite | |
| HET Code: | X4Z |
|---|---|
| Formula: | C25H30N8OS |
| Molecular weight: | 490.624 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.1 % |
| Polar Surface area: | 129.49 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 15.0806 | -15.2504 | 13.5154 |
Image generated by PoseView
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
| Ligand | Protein | Interaction | |||
|---|---|---|---|---|---|
| Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
| C14 | CG2 | ILE- 276 | 4.14 | 0 | Hydrophobic |
| C25 | CG2 | ILE- 276 | 3.84 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 284 | 4.28 | 0 | Hydrophobic |
| C25 | CB | VAL- 284 | 3.9 | 0 | Hydrophobic |
| C31 | CG2 | VAL- 284 | 3.75 | 0 | Hydrophobic |
| C10 | CB | ALA- 297 | 3.76 | 0 | Hydrophobic |
| C29 | CD | LYS- 299 | 3.55 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 328 | 3.98 | 0 | Hydrophobic |
| C10 | CG | MET- 344 | 3.81 | 0 | Hydrophobic |
| C11 | CB | MET- 344 | 4.15 | 0 | Hydrophobic |
| N6 | O | GLU- 345 | 2.85 | 153.15 | H-Bond (Ligand Donor) |
| S19 | CE1 | TYR- 346 | 4.39 | 0 | Hydrophobic |
| N7 | O | LEU- 347 | 2.77 | 166.65 | H-Bond (Ligand Donor) |
| N8 | N | LEU- 347 | 3.01 | 167.35 | H-Bond (Protein Donor) |
| C11 | CD1 | LEU- 396 | 3.7 | 0 | Hydrophobic |
