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
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: | 20.972 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.122 | 516.375 |
| % Hydrophobic | % Polar |
|---|---|
| 48.37 | 51.63 |
| According to VolSite | |
| HET Code: | 3Q5 |
|---|---|
| Formula: | C22H30N8O2 |
| Molecular weight: | 438.526 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.93 % |
| Polar Surface area: | 148.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -45.756 | 18.6126 | 12.0028 |
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 |
| C1 | CB | LEU- 88 | 4.17 | 0 | Hydrophobic |
| C19 | CB | PHE- 93 | 3.74 | 0 | Hydrophobic |
| C19 | CB | SER- 94 | 4.44 | 0 | Hydrophobic |
| O31 | OG | SER- 94 | 2.88 | 132.23 | H-Bond (Protein Donor) |
| C4 | CG2 | VAL- 96 | 3.55 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 96 | 4.1 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 96 | 4.2 | 0 | Hydrophobic |
| C7 | CB | ALA- 109 | 3.8 | 0 | Hydrophobic |
| N24 | NZ | LYS- 111 | 2.9 | 142.03 | H-Bond (Protein Donor) |
| O31 | NZ | LYS- 111 | 2.87 | 163.02 | H-Bond (Protein Donor) |
| C19 | CD2 | LEU- 113 | 3.78 | 0 | Hydrophobic |
| C20 | CB | LYS- 123 | 4.46 | 0 | Hydrophobic |
| C20 | CB | TYR- 126 | 3.75 | 0 | Hydrophobic |
| C21 | CB | TYR- 126 | 4.13 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 127 | 4.25 | 0 | Hydrophobic |
| C21 | CG2 | VAL- 127 | 4.27 | 0 | Hydrophobic |
| N29 | OE2 | GLU- 130 | 2.9 | 171.89 | H-Bond (Ligand Donor) |
| C3 | CD1 | LEU- 159 | 4.24 | 0 | Hydrophobic |
| N26 | O | SER- 160 | 2.96 | 143.28 | H-Bond (Ligand Donor) |
| N25 | N | ALA- 162 | 2.88 | 170.38 | H-Bond (Protein Donor) |
| N28 | O | ALA- 162 | 3.16 | 132.42 | H-Bond (Ligand Donor) |
| C5 | CD1 | LEU- 212 | 3.4 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 212 | 3.36 | 0 | Hydrophobic |
| C4 | CG2 | THR- 222 | 4.46 | 0 | Hydrophobic |
| C6 | CG2 | THR- 222 | 3.98 | 0 | Hydrophobic |
| N23 | OG1 | THR- 222 | 2.7 | 150.95 | H-Bond (Protein Donor) |
| C15 | CB | ASP- 223 | 4.33 | 0 | Hydrophobic |
