sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.920 Å
X-ray
2011-05-09
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.220 | 9.220 | 9.220 | 0.000 | 9.220 | 1 |
| 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: | 18.911 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 5 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.862 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.20 | 53.80 |
| According to VolSite | |
| HET Code: | ABQ |
|---|---|
| Formula: | C24H24FN7O2 |
| Molecular weight: | 461.491 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.44 % |
| Polar Surface area: | 120.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 37.129 | 26.9623 | 28.081 |
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 |
| C24 | CB | LEU- 88 | 4.16 | 0 | Hydrophobic |
| C9 | CG1 | VAL- 96 | 4.26 | 0 | Hydrophobic |
| F34 | CG2 | VAL- 96 | 3.3 | 0 | Hydrophobic |
| C9 | CB | ALA- 109 | 4.35 | 0 | Hydrophobic |
| N25 | NZ | LYS- 111 | 2.69 | 159.5 | H-Bond (Protein Donor) |
| N30 | O | SER- 160 | 2.95 | 166.44 | H-Bond (Ligand Donor) |
| N27 | N | ALA- 162 | 3.01 | 162.34 | H-Bond (Protein Donor) |
| C23 | CG | GLU- 166 | 3.75 | 0 | Hydrophobic |
| C18 | CG | GLU- 209 | 4.13 | 0 | Hydrophobic |
| C19 | CG | GLU- 209 | 4.16 | 0 | Hydrophobic |
| C19 | CB | ASN- 210 | 3.86 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 212 | 3.27 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 212 | 4.05 | 0 | Hydrophobic |
| O32 | OG1 | THR- 222 | 2.9 | 178.61 | H-Bond (Protein Donor) |
| C21 | CB | ASP- 223 | 4.1 | 0 | Hydrophobic |
