sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2003-12-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.160 | 6.160 | 6.160 | 0.000 | 6.160 | 2 |
| 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: | 15.803 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.751 | 533.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.20 | 53.80 |
| According to VolSite | |
| HET Code: | LY4 |
|---|---|
| Formula: | C28H29N4O3 |
| Molecular weight: | 469.555 g/mol |
| DrugBank ID: | DB11829 |
| Buried Surface Area: | 63.84 % |
| Polar Surface area: | 69.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 25.4374 | 79.6479 | 28.4794 |
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 |
| CBA | CB | LEU- 88 | 3.97 | 0 | Hydrophobic |
| CAK | CD1 | LEU- 88 | 3.99 | 0 | Hydrophobic |
| CAQ | CD2 | LEU- 88 | 4.22 | 0 | Hydrophobic |
| CAS | CB | LEU- 88 | 3.76 | 0 | Hydrophobic |
| CAP | CD | LYS- 111 | 3.85 | 0 | Hydrophobic |
| CAO | CD1 | LEU- 159 | 3.81 | 0 | Hydrophobic |
| NAD | O | SER- 160 | 2.84 | 151.96 | H-Bond (Ligand Donor) |
| OAB | N | ALA- 162 | 3.07 | 164.84 | H-Bond (Protein Donor) |
| CBD | CG | GLU- 166 | 4.35 | 0 | Hydrophobic |
| CBD | CG | GLU- 209 | 3.76 | 0 | Hydrophobic |
| CBB | CG2 | THR- 222 | 4.11 | 0 | Hydrophobic |
| CAX | CG2 | THR- 222 | 3.49 | 0 | Hydrophobic |
| OAF | OG1 | THR- 222 | 2.96 | 147.65 | H-Bond (Protein Donor) |
| CAY | CB | ASP- 223 | 3.71 | 0 | Hydrophobic |
