sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.490 Å
X-ray
2011-01-17
| 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: | 38.416 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.669 | 448.875 |
| % Hydrophobic | % Polar |
|---|---|
| 49.62 | 50.38 |
| According to VolSite | |
| HET Code: | 3Q1 |
|---|---|
| Formula: | C15H17N7O |
| Molecular weight: | 311.342 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.57 % |
| Polar Surface area: | 118.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -43.8583 | 17.5171 | 11.9487 |
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 |
| C9 | CB | LEU- 88 | 4.25 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 96 | 3.4 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 96 | 4.4 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 96 | 4.46 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 96 | 3.91 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 96 | 4.22 | 0 | Hydrophobic |
| C5 | CB | ALA- 109 | 3.95 | 0 | Hydrophobic |
| N14 | NZ | LYS- 111 | 2.7 | 170.92 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 111 | 3.86 | 115.04 | Pi/Cation |
| N16 | OE2 | GLU- 130 | 2.95 | 167.74 | H-Bond (Ligand Donor) |
| C6 | CD1 | LEU- 159 | 4.05 | 0 | Hydrophobic |
| N4 | O | SER- 160 | 2.86 | 128.42 | H-Bond (Ligand Donor) |
| N3 | N | ALA- 162 | 3.01 | 168.25 | H-Bond (Protein Donor) |
| N1 | O | ALA- 162 | 3.26 | 132.59 | H-Bond (Ligand Donor) |
| C10 | CD1 | LEU- 212 | 3.34 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 212 | 3.4 | 0 | Hydrophobic |
| N17 | OG1 | THR- 222 | 2.79 | 150.33 | H-Bond (Protein Donor) |
| C7 | CG2 | THR- 222 | 4.03 | 0 | Hydrophobic |
| C23 | CB | ASP- 223 | 4.3 | 0 | Hydrophobic |
