sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2013-08-19
| 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: | 33.367 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.440 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 68.00 | 32.00 |
| According to VolSite | |
| HET Code: | 26L |
|---|---|
| Formula: | C22H24N5 |
| Molecular weight: | 358.459 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.73 % |
| Polar Surface area: | 69.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 41.1051 | 2.77678 | 1.58515 |
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 |
| C4 | CB | LEU- 44 | 4.17 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 44 | 3.86 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 44 | 3.79 | 0 | Hydrophobic |
| C6 | CZ | PHE- 49 | 4.5 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 52 | 3.93 | 0 | Hydrophobic |
| C17 | CB | ALA- 65 | 3.47 | 0 | Hydrophobic |
| N4 | NZ | LYS- 67 | 3.04 | 169.66 | H-Bond (Protein Donor) |
| C18 | CG2 | ILE- 104 | 4.14 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 120 | 4.09 | 0 | Hydrophobic |
| C18 | CB | LEU- 120 | 4.48 | 0 | Hydrophobic |
| C15 | CG | ARG- 122 | 3.71 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 126 | 3.98 | 0 | Hydrophobic |
| C2 | CB | ASP- 128 | 4.19 | 0 | Hydrophobic |
| N1 | O | GLU- 171 | 2.77 | 136.28 | H-Bond (Ligand Donor) |
| C13 | CD2 | LEU- 174 | 4.12 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 174 | 3.57 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 185 | 4.12 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 185 | 3.73 | 0 | Hydrophobic |
