sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-11-27
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.960 | 7.960 | 7.960 | 0.000 | 7.960 | 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: | 28.341 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.263 | 580.500 |
| % Hydrophobic | % Polar |
|---|---|
| 62.79 | 37.21 |
| According to VolSite | |
| HET Code: | VX2 |
|---|---|
| Formula: | C18H18F3N5 |
| Molecular weight: | 361.364 g/mol |
| DrugBank ID: | DB08708 |
| Buried Surface Area: | 60.98 % |
| Polar Surface area: | 55.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -18.8787 | 37.1984 | -1.51958 |
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 |
| C17 | CB | LEU- 44 | 4.05 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 44 | 3.21 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 52 | 4.08 | 0 | Hydrophobic |
| F2 | CG1 | VAL- 52 | 4.41 | 0 | Hydrophobic |
| F1 | CB | ALA- 65 | 3.55 | 0 | Hydrophobic |
| C3 | CB | ALA- 65 | 3.52 | 0 | Hydrophobic |
| C2 | CB | ALA- 65 | 3.77 | 0 | Hydrophobic |
| N2 | NZ | LYS- 67 | 2.93 | 149.17 | H-Bond (Protein Donor) |
| DuAr | NZ | LYS- 67 | 3.96 | 105.94 | Pi/Cation |
| C5 | CG1 | ILE- 104 | 4.03 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 104 | 3.56 | 0 | Hydrophobic |
| C4 | CB | LEU- 120 | 3.75 | 0 | Hydrophobic |
| F1 | CD | ARG- 122 | 3.38 | 0 | Hydrophobic |
| F3 | CG1 | VAL- 126 | 3.96 | 0 | Hydrophobic |
| C15 | CB | ASP- 128 | 4.41 | 0 | Hydrophobic |
| F3 | CD2 | LEU- 174 | 3.4 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 174 | 3.69 | 0 | Hydrophobic |
| C2 | CD2 | LEU- 174 | 3.8 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 174 | 4.41 | 0 | Hydrophobic |
| C5 | CG2 | ILE- 185 | 3.98 | 0 | Hydrophobic |
| C6 | CD1 | ILE- 185 | 4.19 | 0 | Hydrophobic |
| N1 | O | HOH- 334 | 2.91 | 179.99 | H-Bond (Protein Donor) |
