sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.800 Å
X-ray
2009-09-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.000 | 9.000 | 9.000 | 0.000 | 9.000 | 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: | 32.088 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.973 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 54.79 | 45.21 |
| According to VolSite | |
| HET Code: | LXG |
|---|---|
| Formula: | C18H20N3OS |
| Molecular weight: | 326.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 59.16 % |
| Polar Surface area: | 74.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -23.0578 | -34.8036 | -0.826174 |
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 |
| C8 | CD1 | LEU- 44 | 4.44 | 0 | Hydrophobic |
| C13 | CD2 | LEU- 44 | 4.2 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 52 | 4.16 | 0 | Hydrophobic |
| C15 | CB | ALA- 65 | 3.6 | 0 | Hydrophobic |
| O1 | NZ | LYS- 67 | 2.56 | 156.61 | H-Bond (Protein Donor) |
| N3 | NZ | LYS- 67 | 3.06 | 132.7 | H-Bond (Protein Donor) |
| S1 | CG2 | ILE- 104 | 4.29 | 0 | Hydrophobic |
| C15 | CD1 | ILE- 104 | 3.8 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 120 | 3.6 | 0 | Hydrophobic |
| C14 | CB | ARG- 122 | 4.41 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 126 | 3.61 | 0 | Hydrophobic |
| C12 | CB | ASP- 128 | 4.41 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 174 | 4.44 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 174 | 3.41 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 185 | 4.08 | 0 | Hydrophobic |
| S1 | CG2 | ILE- 185 | 3.98 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 186 | 3.38 | 0 | Ionic (Ligand Cationic) |
