sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.950 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: | 21.695 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.845 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.33 | 56.67 |
| According to VolSite | |
| HET Code: | BI3 |
|---|---|
| Formula: | C23H21N4O2 |
| Molecular weight: | 385.438 g/mol |
| DrugBank ID: | DB07457 |
| Buried Surface Area: | 61.71 % |
| Polar Surface area: | 94.53 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 25.7401 | 79.4143 | 28.1074 |
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 | 3.81 | 0 | Hydrophobic |
| CAM | CG1 | VAL- 96 | 4.47 | 0 | Hydrophobic |
| CAC | CG2 | VAL- 96 | 4.24 | 0 | Hydrophobic |
| CAP | CB | VAL- 96 | 3.89 | 0 | Hydrophobic |
| CAB | CD | LYS- 111 | 3.82 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 159 | 3.81 | 0 | Hydrophobic |
| NAU | O | SER- 160 | 2.94 | 152.79 | H-Bond (Ligand Donor) |
| OAX | N | ALA- 162 | 3.01 | 155.35 | H-Bond (Protein Donor) |
| NBC | OE1 | GLU- 166 | 2.99 | 0 | Ionic (Ligand Cationic) |
| CBA | CG | GLU- 209 | 4.02 | 0 | Hydrophobic |
| CAY | CG2 | THR- 222 | 3.98 | 0 | Hydrophobic |
| CAE | CG2 | THR- 222 | 3.64 | 0 | Hydrophobic |
| OAZ | OG1 | THR- 222 | 3 | 151.33 | H-Bond (Protein Donor) |
| CAF | CB | ASP- 223 | 3.7 | 0 | Hydrophobic |
