sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.850 Å
X-ray
2006-12-06
| 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: | 21.684 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.265 | 587.250 |
| % Hydrophobic | % Polar |
|---|---|
| 61.49 | 38.51 |
| According to VolSite | |
| HET Code: | MYF |
|---|---|
| Formula: | C15H9O7 |
| Molecular weight: | 301.228 g/mol |
| DrugBank ID: | DB08230 |
| Buried Surface Area: | 56.28 % |
| Polar Surface area: | 130.28 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 75.6279 | 35.6505 | 0.949136 |
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 |
| O17 | O | HOH- 3 | 2.67 | 179.98 | H-Bond (Protein Donor) |
| C11 | CB | LEU- 44 | 4.29 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 44 | 3.91 | 0 | Hydrophobic |
| C13 | CB | LEU- 44 | 3.77 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 52 | 4.38 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 52 | 3.57 | 0 | Hydrophobic |
| O20 | NZ | LYS- 67 | 3.03 | 138.94 | H-Bond (Protein Donor) |
| C2 | CD | LYS- 67 | 4.07 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 120 | 4.04 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 126 | 4.05 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 174 | 4.25 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 185 | 3.93 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 185 | 3.74 | 0 | Hydrophobic |
| C2 | CB | ILE- 185 | 3.94 | 0 | Hydrophobic |
| C3 | CB | ASP- 186 | 4.27 | 0 | Hydrophobic |
