sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2013-10-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.800 | 7.800 | 7.800 | 0.000 | 7.800 | 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: | 31.531 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.178 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 64.54 | 35.46 |
| According to VolSite | |
| HET Code: | 2HW |
|---|---|
| Formula: | C15H21N7O |
| Molecular weight: | 315.374 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 71.73 % |
| Polar Surface area: | 125.92 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 2 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -18.2944 | 36.5211 | -1.51917 |
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 |
| C2 | CB | LEU- 44 | 4.22 | 0 | Hydrophobic |
| C6 | CB | PHE- 49 | 4.22 | 0 | Hydrophobic |
| C3 | CZ | PHE- 49 | 4.17 | 0 | Hydrophobic |
| C4 | CZ | PHE- 49 | 4.44 | 0 | Hydrophobic |
| C6 | CD1 | PHE- 49 | 3.46 | 0 | Hydrophobic |
| C3 | CB | VAL- 52 | 4.03 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 52 | 4 | 0 | Hydrophobic |
| N2 | NZ | LYS- 67 | 2.83 | 161.8 | H-Bond (Protein Donor) |
| N6 | O | GLU- 121 | 2.77 | 166.49 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 128 | 2.76 | 162.75 | H-Bond (Ligand Donor) |
| N | OD2 | ASP- 128 | 2.76 | 0 | Ionic (Ligand Cationic) |
| N | O | GLU- 171 | 2.75 | 166.25 | H-Bond (Ligand Donor) |
| C4 | CD1 | ILE- 185 | 3.69 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 185 | 3.66 | 0 | Hydrophobic |
| C6 | CB | ASP- 186 | 4.1 | 0 | Hydrophobic |
