sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2010-02-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.440 | 7.700 | 7.760 | 0.160 | 7.820 | 4 |
| 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: | 23.819 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.998 | 337.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.00 | 48.00 |
| According to VolSite | |
| HET Code: | X4Z |
|---|---|
| Formula: | C25H30N8OS |
| Molecular weight: | 490.624 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.4 % |
| 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 |
|---|---|---|
| 20.5607 | 20.4744 | 59.0001 |
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 | CD1 | ILE- 327 | 4.23 | 0 | Hydrophobic |
| C25 | CG1 | ILE- 327 | 4.02 | 0 | Hydrophobic |
| C31 | CB | THR- 332 | 4.27 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 335 | 4.21 | 0 | Hydrophobic |
| C25 | CB | VAL- 335 | 3.93 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 335 | 3.41 | 0 | Hydrophobic |
| C11 | CB | ALA- 348 | 3.69 | 0 | Hydrophobic |
| C33 | CD | LYS- 350 | 3.61 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 379 | 3.93 | 0 | Hydrophobic |
| C10 | CE | MET- 395 | 3.65 | 0 | Hydrophobic |
| C11 | SD | MET- 395 | 3.88 | 0 | Hydrophobic |
| N6 | O | GLU- 396 | 2.76 | 154.73 | H-Bond (Ligand Donor) |
| S19 | CE1 | PHE- 397 | 4.16 | 0 | Hydrophobic |
| N7 | O | LEU- 398 | 3.07 | 166.86 | H-Bond (Ligand Donor) |
| N8 | N | LEU- 398 | 2.83 | 173.66 | H-Bond (Protein Donor) |
| C10 | CD1 | LEU- 447 | 3.72 | 0 | Hydrophobic |
| N30 | OD2 | ASP- 458 | 2.73 | 173.64 | H-Bond (Ligand Donor) |
| N30 | OD2 | ASP- 458 | 2.73 | 0 | Ionic (Ligand Cationic) |
| N30 | OD1 | ASP- 458 | 3.68 | 0 | Ionic (Ligand Cationic) |
| O17 | O | HOH- 2142 | 2.6 | 157.72 | H-Bond (Protein Donor) |
