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
2012-09-01
| 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: | 34.336 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 24 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.986 | 374.625 |
| % Hydrophobic | % Polar |
|---|---|
| 62.16 | 37.84 |
| According to VolSite | |
| HET Code: | 3RA |
|---|---|
| Formula: | C17H14N3O3 |
| Molecular weight: | 308.311 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.1 % |
| Polar Surface area: | 73.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| 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 |
|---|---|---|
| -19.7766 | 37.6317 | -0.0517391 |
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 |
| CAV | CD1 | LEU- 44 | 4.07 | 0 | Hydrophobic |
| CAD | CB | LEU- 44 | 4.02 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 44 | 3.49 | 0 | Hydrophobic |
| CAE | CB | VAL- 52 | 3.85 | 0 | Hydrophobic |
| CAF | CG2 | VAL- 52 | 4.17 | 0 | Hydrophobic |
| CAO | CB | ALA- 65 | 3.69 | 0 | Hydrophobic |
| CAT | CD1 | ILE- 104 | 4.28 | 0 | Hydrophobic |
| CAT | CB | ARG- 122 | 4.05 | 0 | Hydrophobic |
| CAS | CG | ARG- 122 | 3.35 | 0 | Hydrophobic |
| CAV | CB | VAL- 126 | 4.3 | 0 | Hydrophobic |
| CAR | CG1 | VAL- 126 | 3.48 | 0 | Hydrophobic |
| CAT | CD1 | LEU- 174 | 3.29 | 0 | Hydrophobic |
| CAF | CD1 | ILE- 185 | 4.08 | 0 | Hydrophobic |
| NAG | OD1 | ASP- 186 | 3.47 | 130.59 | H-Bond (Ligand Donor) |
| NAG | OD2 | ASP- 186 | 2.72 | 145.05 | H-Bond (Ligand Donor) |
| NAL | OD1 | ASP- 186 | 2.68 | 165.72 | H-Bond (Ligand Donor) |
