sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-04-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.190 | 7.190 | 7.190 | 0.000 | 7.190 | 1 |
| Name: | Serine/threonine-protein kinase PAK 4 |
|---|---|
| ID: | PAK4_HUMAN |
| AC: | O96013 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.974 |
|---|---|
| Number of residues: | 42 |
| Including | |
| Standard Amino Acids: | 40 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.989 | 388.125 |
| % Hydrophobic | % Polar |
|---|---|
| 53.91 | 46.09 |
| According to VolSite | |
| HET Code: | N53 |
|---|---|
| Formula: | C33H37N6O3 |
| Molecular weight: | 565.685 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.46 % |
| Polar Surface area: | 95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 44.8022 | 20.1182 | 17.7719 |
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 |
| C16 | CG2 | THR- 332 | 4 | 0 | Hydrophobic |
| C32 | CG1 | VAL- 335 | 4.01 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 335 | 3.45 | 0 | Hydrophobic |
| C32 | CB | ALA- 348 | 3.71 | 0 | Hydrophobic |
| C13 | CD | LYS- 350 | 3.66 | 0 | Hydrophobic |
| C18 | CG | LYS- 350 | 3.63 | 0 | Hydrophobic |
| C15 | CD | LYS- 350 | 3.66 | 0 | Hydrophobic |
| C17 | CG | MET- 352 | 4.46 | 0 | Hydrophobic |
| C16 | CE | MET- 352 | 4.15 | 0 | Hydrophobic |
| C33 | CG1 | VAL- 379 | 3.91 | 0 | Hydrophobic |
| C32 | SD | MET- 395 | 4.02 | 0 | Hydrophobic |
| C33 | SD | MET- 395 | 3.74 | 0 | Hydrophobic |
| N29 | O | GLU- 396 | 2.72 | 149.71 | H-Bond (Ligand Donor) |
| N30 | N | LEU- 398 | 2.79 | 174.32 | H-Bond (Protein Donor) |
| N38 | O | LEU- 398 | 3.02 | 156.54 | H-Bond (Ligand Donor) |
| C2 | CB | ASP- 405 | 4.01 | 0 | Hydrophobic |
| C33 | CD1 | LEU- 447 | 3.77 | 0 | Hydrophobic |
| N22 | OD2 | ASP- 458 | 2.77 | 147.15 | H-Bond (Ligand Donor) |
| N22 | OD2 | ASP- 458 | 2.77 | 0 | Ionic (Ligand Cationic) |
| N22 | OD1 | ASP- 458 | 3.8 | 0 | Ionic (Ligand Cationic) |
| C4 | CD | ARG- 586 | 3.66 | 0 | Hydrophobic |
| O35 | O | HOH- 2179 | 2.51 | 179.97 | H-Bond (Protein Donor) |
