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
2005-01-11
| 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: | 39.493 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.038 | 610.875 |
| % Hydrophobic | % Polar |
|---|---|
| 55.80 | 44.20 |
| According to VolSite | |
| HET Code: | LY2 |
|---|---|
| Formula: | C19H17NO3 |
| Molecular weight: | 307.343 g/mol |
| DrugBank ID: | DB02656 |
| Buried Surface Area: | 61.78 % |
| Polar Surface area: | 38.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -19.3115 | 36.6919 | -0.90013 |
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 |
| C16 | CB | LEU- 44 | 4.46 | 0 | Hydrophobic |
| C24 | CD1 | LEU- 44 | 3.49 | 0 | Hydrophobic |
| C18 | CZ | PHE- 49 | 3.73 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 52 | 3.79 | 0 | Hydrophobic |
| C25 | CB | ALA- 65 | 4.41 | 0 | Hydrophobic |
| C6 | CB | ALA- 65 | 3.7 | 0 | Hydrophobic |
| O13 | NZ | LYS- 67 | 3.36 | 159.23 | H-Bond (Protein Donor) |
| C2 | CG2 | ILE- 104 | 3.93 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 104 | 3.69 | 0 | Hydrophobic |
| C1 | CB | LEU- 120 | 3.62 | 0 | Hydrophobic |
| C2 | CG | LEU- 120 | 3.67 | 0 | Hydrophobic |
| C24 | CD | ARG- 122 | 3.65 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 126 | 3.87 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 174 | 3.59 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 174 | 3.61 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 185 | 4.22 | 0 | Hydrophobic |
| C2 | CG2 | ILE- 185 | 4.16 | 0 | Hydrophobic |
