sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 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: | 21.372 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | CL |
| Ligandability | Volume (Å3) |
|---|---|
| 1.205 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.53 | 39.47 |
| According to VolSite | |
| HET Code: | 7CP |
|---|---|
| Formula: | C18H19Cl2N4O |
| Molecular weight: | 378.276 g/mol |
| DrugBank ID: | DB07242 |
| Buried Surface Area: | 62.19 % |
| Polar Surface area: | 62.26 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: | 0 |
| X | Y | Z |
|---|---|---|
| 31.5092 | 48.8756 | 14.7439 |
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 |
| C1B | CB | LEU- 44 | 4.02 | 0 | Hydrophobic |
| CL1F | CD1 | LEU- 44 | 3.55 | 0 | Hydrophobic |
| C1M | CE1 | PHE- 49 | 3.69 | 0 | Hydrophobic |
| C1U | CG1 | VAL- 52 | 4.48 | 0 | Hydrophobic |
| C1T | CG2 | VAL- 52 | 4.39 | 0 | Hydrophobic |
| C1V | CG1 | VAL- 52 | 4.33 | 0 | Hydrophobic |
| CL1E | CB | ALA- 65 | 3.77 | 0 | Hydrophobic |
| C1H | CB | ALA- 65 | 3.58 | 0 | Hydrophobic |
| C1H | CD1 | ILE- 104 | 4.16 | 0 | Hydrophobic |
| C1I | CD1 | LEU- 120 | 4.04 | 0 | Hydrophobic |
| CL1E | CG | ARG- 122 | 3.6 | 0 | Hydrophobic |
| CL1F | CG1 | VAL- 126 | 4.31 | 0 | Hydrophobic |
| N1W | OD1 | ASN- 172 | 2.73 | 121.66 | H-Bond (Ligand Donor) |
| CL1E | CD1 | LEU- 174 | 3.55 | 0 | Hydrophobic |
| C1Q | CD1 | LEU- 174 | 3.9 | 0 | Hydrophobic |
| C1P | CD1 | LEU- 174 | 3.52 | 0 | Hydrophobic |
| C1L | CD1 | ILE- 185 | 3.36 | 0 | Hydrophobic |
| C1V | CD1 | ILE- 185 | 3.95 | 0 | Hydrophobic |
| C1T | CD1 | ILE- 185 | 3.65 | 0 | Hydrophobic |
| C1L | CB | ASP- 186 | 4.26 | 0 | Hydrophobic |
| C1M | CB | ASP- 186 | 4.31 | 0 | Hydrophobic |
| N1W | OD2 | ASP- 186 | 2.76 | 131.11 | H-Bond (Ligand Donor) |
| N1W | OD2 | ASP- 186 | 2.76 | 0 | Ionic (Ligand Cationic) |
