sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2006-12-19
| 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: | 48.594 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.778 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.42 | 56.58 |
| According to VolSite | |
| HET Code: | VRV |
|---|---|
| Formula: | C18H11BrN2O2 |
| Molecular weight: | 367.196 g/mol |
| DrugBank ID: | DB08705 |
| Buried Surface Area: | 53.83 % |
| Polar Surface area: | 73.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -17.9217 | 35.4737 | -0.59287 |
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 |
| BR23 | CD1 | LEU- 44 | 4.05 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 52 | 4.5 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 52 | 3.96 | 0 | Hydrophobic |
| C1 | CB | ALA- 65 | 3.57 | 0 | Hydrophobic |
| O21 | NZ | LYS- 67 | 2.64 | 140.87 | H-Bond (Protein Donor) |
| C3 | CG1 | ILE- 104 | 4.22 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 104 | 3.62 | 0 | Hydrophobic |
| C2 | CB | LEU- 120 | 3.68 | 0 | Hydrophobic |
| C3 | CG | LEU- 120 | 4.08 | 0 | Hydrophobic |
| BR23 | CG | ARG- 122 | 4.11 | 0 | Hydrophobic |
| BR23 | CG1 | VAL- 126 | 4.36 | 0 | Hydrophobic |
| BR23 | CD2 | LEU- 174 | 3.99 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 174 | 3.57 | 0 | Hydrophobic |
| C3 | CG2 | ILE- 185 | 4.14 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 185 | 4.02 | 0 | Hydrophobic |
