sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.380 Å
X-ray
2013-07-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 1 |
| 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: | 54.697 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.325 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 66.67 | 33.33 |
| According to VolSite | |
| HET Code: | QUE |
|---|---|
| Formula: | C15H8O7 |
| Molecular weight: | 300.220 g/mol |
| DrugBank ID: | DB04216 |
| Buried Surface Area: | 69.03 % |
| Polar Surface area: | 133.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 168.847 | -119.616 | -2.63059 |
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 |
| C2 | CD1 | LEU- 44 | 3.56 | 0 | Hydrophobic |
| C6 | CB | LEU- 44 | 3.98 | 0 | Hydrophobic |
| C19 | CG2 | VAL- 52 | 3.98 | 0 | Hydrophobic |
| C17 | CD | LYS- 67 | 3.73 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 104 | 4.03 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 120 | 3.5 | 0 | Hydrophobic |
| O27 | O | GLU- 121 | 3 | 156.34 | H-Bond (Ligand Donor) |
| C1 | CG1 | VAL- 126 | 3.88 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 174 | 3.61 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 174 | 4.38 | 0 | Hydrophobic |
| C19 | CD1 | ILE- 185 | 3.91 | 0 | Hydrophobic |
| C15 | CG2 | ILE- 185 | 3.68 | 0 | Hydrophobic |
| C16 | CB | ILE- 185 | 3.97 | 0 | Hydrophobic |
| C18 | CB | ASP- 186 | 4.05 | 0 | Hydrophobic |
