sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2003-12-16
| 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: | 17.169 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.738 | 523.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.81 | 54.19 |
| According to VolSite | |
| HET Code: | BI2 |
|---|---|
| Formula: | C27H27N4O2 |
| Molecular weight: | 439.529 g/mol |
| DrugBank ID: | DB07456 |
| Buried Surface Area: | 60.12 % |
| Polar Surface area: | 71.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 20.668 | 87.5655 | 3.91145 |
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 |
| CAS | CB | LEU- 88 | 3.78 | 0 | Hydrophobic |
| CAC | CG2 | VAL- 96 | 4.35 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 96 | 4.5 | 0 | Hydrophobic |
| CAP | CB | VAL- 96 | 4.01 | 0 | Hydrophobic |
| CAB | CD | LYS- 111 | 3.94 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 159 | 3.68 | 0 | Hydrophobic |
| NAU | O | SER- 160 | 2.75 | 160.12 | H-Bond (Ligand Donor) |
| OAX | N | ALA- 162 | 3.13 | 150.73 | H-Bond (Protein Donor) |
| CBA | CG | GLU- 166 | 4.41 | 0 | Hydrophobic |
| CBF | CG | GLU- 209 | 3.79 | 0 | Hydrophobic |
| CBA | CG | GLU- 209 | 4.16 | 0 | Hydrophobic |
| CAY | CG2 | THR- 222 | 4.2 | 0 | Hydrophobic |
| CAE | CG2 | THR- 222 | 3.51 | 0 | Hydrophobic |
| OAZ | OG1 | THR- 222 | 3.08 | 158.92 | H-Bond (Protein Donor) |
| CAF | CB | ASP- 223 | 3.78 | 0 | Hydrophobic |
