sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2008-04-25
| 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: | 29.848 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 1.124 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 56.17 | 43.83 |
| According to VolSite | |
| HET Code: | MB9 |
|---|---|
| Formula: | C17H18ClN4O |
| Molecular weight: | 329.804 g/mol |
| DrugBank ID: | DB08166 |
| Buried Surface Area: | 59.44 % |
| Polar Surface area: | 74.43 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -17.854 | 36.3821 | -0.761304 |
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 |
| C1A | CB | LEU- 44 | 3.91 | 0 | Hydrophobic |
| C1H | CD1 | LEU- 44 | 4.13 | 0 | Hydrophobic |
| C1K | CE1 | PHE- 49 | 3.64 | 0 | Hydrophobic |
| C1U | CG1 | VAL- 52 | 4.31 | 0 | Hydrophobic |
| C1S | CG1 | VAL- 52 | 4.26 | 0 | Hydrophobic |
| C1P | CB | ALA- 65 | 3.72 | 0 | Hydrophobic |
| C1F | CD1 | ILE- 104 | 4.26 | 0 | Hydrophobic |
| C1G | CD1 | LEU- 120 | 4.34 | 0 | Hydrophobic |
| CL1D | CG | ARG- 122 | 3.48 | 0 | Hydrophobic |
| N1M | OD1 | ASN- 172 | 2.88 | 126.31 | H-Bond (Ligand Donor) |
| CL1D | CD1 | LEU- 174 | 3.58 | 0 | Hydrophobic |
| C1P | CD1 | LEU- 174 | 3.63 | 0 | Hydrophobic |
| C1L | CD1 | ILE- 185 | 3.51 | 0 | Hydrophobic |
| C1U | CD1 | ILE- 185 | 3.92 | 0 | Hydrophobic |
| C1S | CD1 | ILE- 185 | 3.62 | 0 | Hydrophobic |
| C1G | CD1 | ILE- 185 | 3.66 | 0 | Hydrophobic |
| C1K | CB | ASP- 186 | 4.34 | 0 | Hydrophobic |
| C1L | CB | ASP- 186 | 4.37 | 0 | Hydrophobic |
| N1M | OD2 | ASP- 186 | 2.98 | 139.43 | H-Bond (Ligand Donor) |
| N1M | OD2 | ASP- 186 | 2.98 | 0 | Ionic (Ligand Cationic) |
