sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.990 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: | 26.319 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.827 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 44.30 | 55.70 |
| According to VolSite | |
| HET Code: | 3Q4 |
|---|---|
| Formula: | C24H26N8O |
| Molecular weight: | 442.516 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 58.04 % |
| Polar Surface area: | 138.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -45.7695 | 19.3839 | 11.5824 |
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 |
| C4 | CB | LEU- 88 | 4.09 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 96 | 3.73 | 0 | Hydrophobic |
| C24 | CG2 | VAL- 96 | 4.06 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 96 | 4 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 96 | 4.21 | 0 | Hydrophobic |
| C12 | CB | ALA- 109 | 3.84 | 0 | Hydrophobic |
| N26 | NZ | LYS- 111 | 2.96 | 140.07 | H-Bond (Protein Donor) |
| C1 | CB | TYR- 126 | 3.77 | 0 | Hydrophobic |
| N31 | OE2 | GLU- 130 | 2.88 | 170.05 | H-Bond (Ligand Donor) |
| C8 | CD1 | LEU- 159 | 4.25 | 0 | Hydrophobic |
| N28 | O | SER- 160 | 2.91 | 141.21 | H-Bond (Ligand Donor) |
| N27 | N | ALA- 162 | 2.92 | 174.47 | H-Bond (Protein Donor) |
| N30 | O | ALA- 162 | 3.1 | 129.36 | H-Bond (Ligand Donor) |
| C10 | CD1 | LEU- 212 | 3.45 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 212 | 3.44 | 0 | Hydrophobic |
| C9 | CG2 | THR- 222 | 4.44 | 0 | Hydrophobic |
| C11 | CG2 | THR- 222 | 4.12 | 0 | Hydrophobic |
| N25 | OG1 | THR- 222 | 2.86 | 150.39 | H-Bond (Protein Donor) |
| N32 | OD1 | ASP- 223 | 2.92 | 138.04 | H-Bond (Ligand Donor) |
| C2 | CG2 | THR- 226 | 3.65 | 0 | Hydrophobic |
