sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.510 Å
X-ray
2003-08-01
| 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: | 22.413 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.295 | 452.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.96 | 41.04 |
| According to VolSite | |
| HET Code: | UCN |
|---|---|
| Formula: | C28H27N4O4 |
| Molecular weight: | 483.538 g/mol |
| DrugBank ID: | DB01933 |
| Buried Surface Area: | 64.7 % |
| Polar Surface area: | 94.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 82.7878 | 17.5383 | 12.3047 |
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 | CD1 | LEU- 88 | 4.01 | 0 | Hydrophobic |
| C19 | CB | LEU- 88 | 4.25 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 88 | 4.12 | 0 | Hydrophobic |
| C20 | CB | LEU- 88 | 3.75 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 88 | 3.96 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 96 | 4.06 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 96 | 3.66 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 96 | 3.87 | 0 | Hydrophobic |
| C7 | CB | ALA- 109 | 4.28 | 0 | Hydrophobic |
| C14 | CD | LYS- 111 | 4.33 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 159 | 3.81 | 0 | Hydrophobic |
| N1 | O | SER- 160 | 2.92 | 177.59 | H-Bond (Ligand Donor) |
| O5 | N | ALA- 162 | 2.78 | 168.46 | H-Bond (Protein Donor) |
| C24 | CG | GLU- 166 | 4.17 | 0 | Hydrophobic |
| N4 | OE2 | GLU- 166 | 2.6 | 165.96 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 166 | 2.6 | 0 | Ionic (Ligand Cationic) |
| N4 | O | GLU- 209 | 3.15 | 145.71 | H-Bond (Ligand Donor) |
| C27 | CD2 | LEU- 212 | 4.14 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 212 | 3.28 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 212 | 3.28 | 0 | Hydrophobic |
| O37 | OG1 | THR- 222 | 2.97 | 149.59 | H-Bond (Protein Donor) |
| C27 | CG2 | THR- 222 | 3.89 | 0 | Hydrophobic |
| C12 | CG2 | THR- 222 | 4.09 | 0 | Hydrophobic |
| C27 | CB | ASP- 223 | 4.39 | 0 | Hydrophobic |
| C15 | CB | ASP- 223 | 3.96 | 0 | Hydrophobic |
