sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2012-01-02
| 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: | 33.777 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.269 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 65.41 | 34.59 |
| According to VolSite | |
| HET Code: | 0F5 |
|---|---|
| Formula: | C20H22N5O2S |
| Molecular weight: | 396.486 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.47 % |
| Polar Surface area: | 124.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -22.8886 | -34.2175 | -0.808179 |
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 |
| O19 | O | HOH- 20 | 2.91 | 179.94 | H-Bond (Protein Donor) |
| C09 | CD1 | LEU- 44 | 4.16 | 0 | Hydrophobic |
| C22 | CZ | PHE- 49 | 3.42 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 49 | 3.24 | 0 | Hydrophobic |
| S18 | CG2 | VAL- 52 | 3.79 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 52 | 4.37 | 0 | Hydrophobic |
| C10 | CB | ALA- 65 | 3.49 | 0 | Hydrophobic |
| N16 | NZ | LYS- 67 | 2.9 | 166.1 | H-Bond (Protein Donor) |
| O20 | NZ | LYS- 67 | 3.16 | 129.75 | H-Bond (Protein Donor) |
| C10 | CD1 | ILE- 104 | 3.82 | 0 | Hydrophobic |
| C10 | CB | LEU- 120 | 4.34 | 0 | Hydrophobic |
| C08 | CB | ARG- 122 | 3.98 | 0 | Hydrophobic |
| C09 | CG | ARG- 122 | 4.21 | 0 | Hydrophobic |
| C09 | CD1 | LEU- 174 | 3.59 | 0 | Hydrophobic |
| S18 | CD1 | ILE- 185 | 4.08 | 0 | Hydrophobic |
| C12 | CG2 | ILE- 185 | 4.11 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 185 | 3.86 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 185 | 3.62 | 0 | Hydrophobic |
| O19 | N | ASP- 186 | 2.98 | 161.39 | H-Bond (Protein Donor) |
| N27 | OD1 | ASP- 186 | 3.04 | 0 | Ionic (Ligand Cationic) |
