sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2007-11-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.260 | 6.260 | 6.260 | 0.000 | 6.260 | 1 |
| Name: | Serine/threonine-protein kinase pim-1 |
|---|---|
| ID: | PIM1_HUMAN |
| AC: | P11309 |
| 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: | 34.000 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.270 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 63.45 | 36.55 |
| According to VolSite | |
| HET Code: | VX3 |
|---|---|
| Formula: | C21H14NO2 |
| Molecular weight: | 312.341 g/mol |
| DrugBank ID: | DB08709 |
| Buried Surface Area: | 59.72 % |
| Polar Surface area: | 55.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -18.9845 | 37.1319 | -1.08496 |
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 |
| C12 | CB | LEU- 44 | 3.87 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 44 | 3.51 | 0 | Hydrophobic |
| C14 | CZ | PHE- 49 | 3.29 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 52 | 3.85 | 0 | Hydrophobic |
| C12 | CB | VAL- 52 | 4.48 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 52 | 4.47 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 52 | 4.02 | 0 | Hydrophobic |
| C18 | CB | ALA- 65 | 4.44 | 0 | Hydrophobic |
| C24 | CB | ALA- 65 | 3.79 | 0 | Hydrophobic |
| O2 | NZ | LYS- 67 | 2.7 | 154.98 | H-Bond (Protein Donor) |
| O4 | NZ | LYS- 67 | 3.46 | 146.81 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 67 | 2.7 | 0 | Ionic (Protein Cationic) |
| O4 | NZ | LYS- 67 | 3.46 | 0 | Ionic (Protein Cationic) |
| C25 | CG1 | ILE- 104 | 3.68 | 0 | Hydrophobic |
| C25 | CB | LEU- 120 | 3.99 | 0 | Hydrophobic |
| C26 | CG | LEU- 120 | 3.65 | 0 | Hydrophobic |
| C19 | CD | ARG- 122 | 4.03 | 0 | Hydrophobic |
| C20 | CG1 | VAL- 126 | 3.57 | 0 | Hydrophobic |
| C17 | CD2 | LEU- 174 | 4.24 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 174 | 4.09 | 0 | Hydrophobic |
| C24 | CD2 | LEU- 174 | 3.58 | 0 | Hydrophobic |
| C5 | CB | ILE- 185 | 3.79 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 185 | 4.49 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 185 | 3.72 | 0 | Hydrophobic |
| C26 | CG2 | ILE- 185 | 3.64 | 0 | Hydrophobic |
| O4 | N | ASP- 186 | 3.01 | 143.31 | H-Bond (Protein Donor) |
| O4 | O | HOH- 321 | 2.83 | 179.95 | H-Bond (Protein Donor) |
