sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2013-07-10
| 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: | 35.717 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.504 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 68.67 | 31.33 |
| According to VolSite | |
| HET Code: | Q17 |
|---|---|
| Formula: | C17H19N4O |
| Molecular weight: | 295.359 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.97 % |
| Polar Surface area: | 85.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 40.9513 | 2.43159 | -0.994591 |
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 |
| C17 | CD1 | LEU- 44 | 3.76 | 0 | Hydrophobic |
| C3 | CG | PHE- 49 | 3.32 | 0 | Hydrophobic |
| C3 | CB | PHE- 49 | 3.49 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 52 | 4.2 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 52 | 3.68 | 0 | Hydrophobic |
| C14 | CB | ALA- 65 | 3.5 | 0 | Hydrophobic |
| C2 | CD | LYS- 67 | 3.48 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 104 | 4.4 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 120 | 4.24 | 0 | Hydrophobic |
| C15 | CB | ARG- 122 | 3.88 | 0 | Hydrophobic |
| C16 | CG | ARG- 122 | 4 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 126 | 4.24 | 0 | Hydrophobic |
| N22 | OD1 | ASP- 128 | 2.69 | 157 | H-Bond (Ligand Donor) |
| N22 | OD1 | ASP- 128 | 2.69 | 0 | Ionic (Ligand Cationic) |
| N22 | O | GLU- 171 | 2.84 | 144.52 | H-Bond (Ligand Donor) |
| C16 | CD1 | LEU- 174 | 3.57 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 185 | 4.46 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 185 | 3.84 | 0 | Hydrophobic |
| C6 | CB | ILE- 185 | 3.91 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 185 | 3.93 | 0 | Hydrophobic |
| C2 | CB | ASP- 186 | 3.48 | 0 | Hydrophobic |
