sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.550 Å
X-ray
2011-11-15
| 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: | 39.590 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.886 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.25 | 44.75 |
| According to VolSite | |
| HET Code: | Q18 |
|---|---|
| Formula: | C24H25N2O3 |
| Molecular weight: | 389.467 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.07 % |
| Polar Surface area: | 66.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 22.4417 | 33.7875 | -0.499655 |
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 |
| C26 | CD1 | LEU- 44 | 3.67 | 0 | Hydrophobic |
| C13 | CZ | PHE- 49 | 2.81 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 52 | 4.03 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 52 | 3.85 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 52 | 4.16 | 0 | Hydrophobic |
| C21 | CB | ALA- 65 | 3.58 | 0 | Hydrophobic |
| O28 | NZ | LYS- 67 | 2.5 | 144.95 | H-Bond (Protein Donor) |
| C18 | CD1 | LEU- 120 | 3.55 | 0 | Hydrophobic |
| N22 | O | GLU- 121 | 2.78 | 141.53 | H-Bond (Ligand Donor) |
| C27 | CG | ARG- 122 | 4.05 | 0 | Hydrophobic |
| C7 | CB | GLU- 171 | 4.33 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 174 | 3.65 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 174 | 3.67 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 185 | 4.01 | 0 | Hydrophobic |
| C12 | CB | ASP- 186 | 3.88 | 0 | Hydrophobic |
