sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2010-07-01
| 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: | 14.977 |
|---|---|
| Number of residues: | 21 |
| Including | |
| Standard Amino Acids: | 19 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 1.045 | 442.125 |
| % Hydrophobic | % Polar |
|---|---|
| 62.60 | 37.40 |
| According to VolSite | |
| HET Code: | XIY |
|---|---|
| Formula: | C8H8N2O |
| Molecular weight: | 148.162 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.62 % |
| Polar Surface area: | 48.91 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| -22.2867 | -35.4903 | -0.170364 |
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 |
| CE3 | CD1 | LEU- 44 | 3.82 | 0 | Hydrophobic |
| C | CE1 | PHE- 49 | 3.68 | 0 | Hydrophobic |
| CE2 | CG1 | VAL- 52 | 4.24 | 0 | Hydrophobic |
| C | CG2 | VAL- 52 | 3.58 | 0 | Hydrophobic |
| CH2 | CB | ALA- 65 | 3.49 | 0 | Hydrophobic |
| CZ2 | CG1 | ILE- 104 | 4.14 | 0 | Hydrophobic |
| CZ2 | CD1 | LEU- 120 | 4.39 | 0 | Hydrophobic |
| CH2 | CB | ARG- 122 | 4.46 | 0 | Hydrophobic |
| CZ3 | CG | ARG- 122 | 4.03 | 0 | Hydrophobic |
| CZ3 | CD1 | LEU- 174 | 3.57 | 0 | Hydrophobic |
| C | CD1 | ILE- 185 | 3.73 | 0 | Hydrophobic |
| CZ2 | CG2 | ILE- 185 | 4.2 | 0 | Hydrophobic |
| O | OD2 | ASP- 186 | 3.41 | 158.02 | H-Bond (Ligand Donor) |
