sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-11-12
| 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: | 23.788 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.425 | 519.750 |
| % Hydrophobic | % Polar |
|---|---|
| 63.64 | 36.36 |
| According to VolSite | |
| HET Code: | E46 |
|---|---|
| Formula: | C18H20F3N6O |
| Molecular weight: | 393.386 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.8 % |
| Polar Surface area: | 81.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -42.0924 | -2.63846 | 1.06464 |
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 |
| FAB | CG | LEU- 44 | 4.33 | 0 | Hydrophobic |
| CBB | CD1 | LEU- 44 | 3.9 | 0 | Hydrophobic |
| CAN | CZ | PHE- 49 | 4.35 | 0 | Hydrophobic |
| CAG | CD1 | PHE- 49 | 3.33 | 0 | Hydrophobic |
| CAH | CB | PHE- 49 | 3.92 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 52 | 4.04 | 0 | Hydrophobic |
| CAG | CG2 | VAL- 52 | 4.05 | 0 | Hydrophobic |
| CAE | CB | ALA- 65 | 3.38 | 0 | Hydrophobic |
| NAO | NZ | LYS- 67 | 3.34 | 162.13 | H-Bond (Protein Donor) |
| CAD | CG1 | ILE- 104 | 3.79 | 0 | Hydrophobic |
| CAF | CB | LEU- 120 | 4.06 | 0 | Hydrophobic |
| FAB | CD | ARG- 122 | 3.8 | 0 | Hydrophobic |
| CAE | CB | ARG- 122 | 4.35 | 0 | Hydrophobic |
| FAC | CG | ARG- 122 | 3.9 | 0 | Hydrophobic |
| FAC | CG1 | VAL- 126 | 3.82 | 0 | Hydrophobic |
| NAR | OD2 | ASP- 128 | 2.59 | 132.64 | H-Bond (Ligand Donor) |
| NAR | OD2 | ASP- 128 | 2.59 | 0 | Ionic (Ligand Cationic) |
| FAA | CD2 | LEU- 174 | 3.95 | 0 | Hydrophobic |
| FAC | CD1 | LEU- 174 | 3.36 | 0 | Hydrophobic |
| CAE | CD1 | LEU- 174 | 3.86 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 185 | 4.48 | 0 | Hydrophobic |
| CAM | CD1 | ILE- 185 | 4.46 | 0 | Hydrophobic |
| CAF | CG2 | ILE- 185 | 4.07 | 0 | Hydrophobic |
| CAH | CB | ASP- 186 | 3.7 | 0 | Hydrophobic |
