sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.980 Å
X-ray
2008-01-29
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 16.522 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.076 | 583.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.27 | 38.73 |
| According to VolSite | |
| HET Code: | C4E |
|---|---|
| Formula: | C13H11N3 |
| Molecular weight: | 209.247 g/mol |
| DrugBank ID: | DB07524 |
| Buried Surface Area: | 69.24 % |
| Polar Surface area: | 40.71 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -6.19006 | 83.1017 | 66.3687 |
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 |
| C1 | CD1 | LEU- 44 | 3.72 | 0 | Hydrophobic |
| C15 | CB | PHE- 49 | 3.62 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 52 | 4.14 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 52 | 4.26 | 0 | Hydrophobic |
| C8 | CB | ALA- 65 | 4.27 | 0 | Hydrophobic |
| C14 | CD | LYS- 67 | 3.45 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 120 | 3.8 | 0 | Hydrophobic |
| N5 | O | GLU- 121 | 3.11 | 174.83 | H-Bond (Ligand Donor) |
| C8 | CD1 | LEU- 174 | 3.88 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 174 | 4.28 | 0 | Hydrophobic |
| C12 | CB | ILE- 185 | 4.28 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 185 | 3.61 | 0 | Hydrophobic |
| C15 | CB | ASP- 186 | 3.43 | 0 | Hydrophobic |
