sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2007-04-01
| Name: | 3-phosphoinositide-dependent protein kinase 1 |
|---|---|
| ID: | PDPK1_HUMAN |
| AC: | O15530 |
| 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: | 21.865 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.696 | 482.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.06 | 55.94 |
| According to VolSite | |
| HET Code: | 39Z |
|---|---|
| Formula: | C14H12N2O2 |
| Molecular weight: | 240.257 g/mol |
| DrugBank ID: | DB07033 |
| Buried Surface Area: | 61.28 % |
| Polar Surface area: | 65.45 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -6.85494 | 42.2703 | 44.3858 |
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 |
| C20 | CB | LEU- 88 | 4.02 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 96 | 4.21 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 96 | 3.95 | 0 | Hydrophobic |
| C7 | CB | ALA- 109 | 4.44 | 0 | Hydrophobic |
| C11 | CB | ALA- 109 | 4.06 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 143 | 4.19 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 159 | 4.15 | 0 | Hydrophobic |
| N1 | O | SER- 160 | 2.86 | 170.11 | H-Bond (Ligand Donor) |
| O4 | N | ALA- 162 | 3.02 | 132.89 | H-Bond (Protein Donor) |
| C11 | CD1 | LEU- 212 | 4.14 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 212 | 4.47 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 212 | 3.6 | 0 | Hydrophobic |
| C9 | CG2 | THR- 222 | 4.05 | 0 | Hydrophobic |
| C10 | CB | THR- 222 | 4.08 | 0 | Hydrophobic |
| O12 | O | HOH- 796 | 2.98 | 164.39 | H-Bond (Ligand Donor) |
