sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2010-09-08
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 22.164 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.675 | 833.625 |
| % Hydrophobic | % Polar |
|---|---|
| 44.94 | 55.06 |
| According to VolSite | |
| HET Code: | BI4 |
|---|---|
| Formula: | C27H27N4O2 |
| Molecular weight: | 439.529 g/mol |
| DrugBank ID: | DB07458 |
| Buried Surface Area: | 65.86 % |
| Polar Surface area: | 71.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 47.2511 | -86.7956 | -17.5618 |
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 |
| C11 | CB | LEU- 88 | 3.72 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 96 | 4.46 | 0 | Hydrophobic |
| C14 | CB | VAL- 96 | 4.05 | 0 | Hydrophobic |
| C27 | CG2 | VAL- 96 | 3.9 | 0 | Hydrophobic |
| C2 | CD | LYS- 111 | 3.93 | 0 | Hydrophobic |
| C2 | CE | MET- 134 | 4.32 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 159 | 3.75 | 0 | Hydrophobic |
| N19 | O | SER- 160 | 2.9 | 168.63 | H-Bond (Ligand Donor) |
| O32 | N | ALA- 162 | 2.89 | 165.18 | H-Bond (Protein Donor) |
| O33 | OG1 | THR- 222 | 3.05 | 148.01 | H-Bond (Protein Donor) |
| C24 | CG2 | THR- 222 | 4.34 | 0 | Hydrophobic |
| C23 | CG2 | THR- 222 | 3.52 | 0 | Hydrophobic |
| C4 | CB | ASP- 223 | 3.83 | 0 | Hydrophobic |
