sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 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: | 32.858 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.339 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 71.01 | 28.99 |
| According to VolSite | |
| HET Code: | JN5 |
|---|---|
| Formula: | C20H16N6S |
| Molecular weight: | 372.446 g/mol |
| DrugBank ID: | DB08022 |
| Buried Surface Area: | 61.93 % |
| Polar Surface area: | 115.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -18.6611 | 36.9509 | -0.914926 |
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 |
| C1X | CD1 | LEU- 44 | 3.81 | 0 | Hydrophobic |
| C1D | CD1 | LEU- 44 | 3.83 | 0 | Hydrophobic |
| C5 | CB | PHE- 49 | 4.29 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 49 | 3.67 | 0 | Aromatic Face/Face |
| S1H | CG1 | VAL- 52 | 3.89 | 0 | Hydrophobic |
| C1F | CG1 | VAL- 52 | 3.9 | 0 | Hydrophobic |
| C1A | CB | ALA- 65 | 3.26 | 0 | Hydrophobic |
| N1L | NZ | LYS- 67 | 2.83 | 163.33 | H-Bond (Protein Donor) |
| C1C | CG1 | ILE- 104 | 3.91 | 0 | Hydrophobic |
| C1A | CD1 | ILE- 104 | 3.74 | 0 | Hydrophobic |
| C1C | CB | LEU- 120 | 4.02 | 0 | Hydrophobic |
| C1B | CG | ARG- 122 | 4.38 | 0 | Hydrophobic |
| C1X | CG1 | VAL- 126 | 3.46 | 0 | Hydrophobic |
| C1U | CB | ASP- 128 | 4.4 | 0 | Hydrophobic |
| C1W | CD2 | LEU- 174 | 3.67 | 0 | Hydrophobic |
| C1W | CD2 | LEU- 174 | 3.67 | 0 | Hydrophobic |
| C1D | CD1 | LEU- 174 | 3.8 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 185 | 4.21 | 0 | Hydrophobic |
| C1E | CG2 | ILE- 185 | 4 | 0 | Hydrophobic |
| S1H | CD1 | ILE- 185 | 3.73 | 0 | Hydrophobic |
| C5 | CB | ASP- 186 | 4.03 | 0 | Hydrophobic |
