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
2010-09-13
| 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: | 37.472 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 0.650 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.45 | 58.55 |
| According to VolSite | |
| HET Code: | BI4 |
|---|---|
| Formula: | C27H27N4O2 |
| Molecular weight: | 439.529 g/mol |
| DrugBank ID: | DB07458 |
| Buried Surface Area: | 59.61 % |
| 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 |
|---|---|---|
| -13.8495 | 2.06788 | -16.0216 |
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 |
| C10 | CB | LEU- 88 | 3.71 | 0 | Hydrophobic |
| C11 | CB | LEU- 88 | 3.72 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 96 | 4.46 | 0 | Hydrophobic |
| C14 | CB | VAL- 96 | 3.99 | 0 | Hydrophobic |
| C2 | CD | LYS- 111 | 4.22 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 159 | 3.64 | 0 | Hydrophobic |
| N19 | O | SER- 160 | 2.79 | 168.74 | H-Bond (Ligand Donor) |
| O32 | N | ALA- 162 | 3.01 | 168.51 | H-Bond (Protein Donor) |
| C27 | CG | GLU- 209 | 3.39 | 0 | Hydrophobic |
| O33 | OG1 | THR- 222 | 2.83 | 147.49 | H-Bond (Protein Donor) |
| C23 | CG2 | THR- 222 | 3.56 | 0 | Hydrophobic |
| C4 | CB | ASP- 223 | 3.78 | 0 | Hydrophobic |
