sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2009-09-04
| 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: | 16.847 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 23 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.110 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.07 | 38.93 |
| According to VolSite | |
| HET Code: | 1DR |
|---|---|
| Formula: | C15H10N2O |
| Molecular weight: | 234.253 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.76 % |
| Polar Surface area: | 48.65 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 26.5748 | 49.902 | 0.419556 |
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 |
| CAB | CD1 | LEU- 44 | 3.55 | 0 | Hydrophobic |
| CAL | CG2 | VAL- 52 | 3.85 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 52 | 4.1 | 0 | Hydrophobic |
| CAE | CB | ALA- 65 | 3.64 | 0 | Hydrophobic |
| CAF | CB | ALA- 65 | 4.08 | 0 | Hydrophobic |
| OAR | NZ | LYS- 67 | 2.74 | 167.48 | H-Bond (Protein Donor) |
| CAK | CD1 | LEU- 120 | 3.92 | 0 | Hydrophobic |
| CAD | CG | ARG- 122 | 3.51 | 0 | Hydrophobic |
| CAC | CG1 | VAL- 126 | 3.83 | 0 | Hydrophobic |
| CAE | CD1 | LEU- 174 | 3.55 | 0 | Hydrophobic |
| CAE | CD1 | LEU- 174 | 3.55 | 0 | Hydrophobic |
| CAJ | CG2 | ILE- 185 | 4 | 0 | Hydrophobic |
| CAK | CB | ILE- 185 | 4.08 | 0 | Hydrophobic |
| CAH | CD1 | ILE- 185 | 3.85 | 0 | Hydrophobic |
| CAM | CD1 | ILE- 185 | 3.61 | 0 | Hydrophobic |
