sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.810 Å
X-ray
2004-01-22
| 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: | 25.441 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.637 | 550.125 |
| % Hydrophobic | % Polar |
|---|---|
| 42.33 | 57.67 |
| According to VolSite | |
| HET Code: | BI8 |
|---|---|
| Formula: | C24H23N4O2 |
| Molecular weight: | 399.465 g/mol |
| DrugBank ID: | DB01946 |
| Buried Surface Area: | 64.49 % |
| Polar Surface area: | 83.66 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 82.4744 | 17.3975 | 12.3353 |
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 |
| CB0 | CD2 | LEU- 88 | 4.37 | 0 | Hydrophobic |
| CAS | CB | LEU- 88 | 3.83 | 0 | Hydrophobic |
| CAP | CG2 | VAL- 96 | 4.17 | 0 | Hydrophobic |
| CAQ | CB | VAL- 96 | 4.47 | 0 | Hydrophobic |
| CAC | CG2 | VAL- 96 | 4.11 | 0 | Hydrophobic |
| CAB | CD | LYS- 111 | 3.83 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 159 | 3.5 | 0 | Hydrophobic |
| NAU | O | SER- 160 | 3.09 | 156.94 | H-Bond (Ligand Donor) |
| OAX | N | ALA- 162 | 3.01 | 144.19 | H-Bond (Protein Donor) |
| NBC | OE2 | GLU- 166 | 2.68 | 137.82 | H-Bond (Ligand Donor) |
| NBC | OE2 | GLU- 166 | 2.68 | 0 | Ionic (Ligand Cationic) |
| NBC | OE1 | GLU- 166 | 3.62 | 0 | Ionic (Ligand Cationic) |
| CBA | CG | GLU- 166 | 4.12 | 0 | Hydrophobic |
| NBC | OE1 | GLU- 209 | 3.99 | 0 | Ionic (Ligand Cationic) |
| CBA | CG | GLU- 209 | 4.16 | 0 | Hydrophobic |
| CBA | CD2 | LEU- 212 | 4.4 | 0 | Hydrophobic |
| CAY | CG2 | THR- 222 | 4 | 0 | Hydrophobic |
| CAE | CG2 | THR- 222 | 3.85 | 0 | Hydrophobic |
| OAZ | OG1 | THR- 222 | 3 | 173.73 | H-Bond (Protein Donor) |
| CAF | CB | ASP- 223 | 3.6 | 0 | Hydrophobic |
