sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2005-10-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.600 | 7.600 | 7.600 | 0.000 | 7.600 | 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 |
|---|---|
| B | 100 % |
| B-Factor: | 30.738 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.386 | 486.000 |
| % Hydrophobic | % Polar |
|---|---|
| 65.97 | 34.03 |
| According to VolSite | |
| HET Code: | IYZ |
|---|---|
| Formula: | C18H19N4O |
| Molecular weight: | 307.370 g/mol |
| DrugBank ID: | DB04715 |
| Buried Surface Area: | 65.68 % |
| Polar Surface area: | 60.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 26.6657 | 50.6561 | 0.269957 |
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 |
| CAJ | CB | LEU- 44 | 4.22 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 44 | 4.25 | 0 | Hydrophobic |
| CAJ | CE1 | PHE- 49 | 4.11 | 0 | Hydrophobic |
| CAK | CZ | PHE- 49 | 4.21 | 0 | Hydrophobic |
| CAJ | CB | VAL- 52 | 3.68 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 52 | 4.16 | 0 | Hydrophobic |
| CAC | CB | ALA- 65 | 3.46 | 0 | Hydrophobic |
| NAM | NZ | LYS- 67 | 3.16 | 170.53 | H-Bond (Protein Donor) |
| CAC | CG2 | ILE- 104 | 3.93 | 0 | Hydrophobic |
| CAE | CB | LEU- 120 | 4.22 | 0 | Hydrophobic |
| CAD | CG | ARG- 122 | 4.4 | 0 | Hydrophobic |
| CAA | CD2 | LEU- 174 | 4.09 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 174 | 3.7 | 0 | Hydrophobic |
| CAD | CD1 | LEU- 174 | 3.6 | 0 | Hydrophobic |
| CAL | CD1 | ILE- 185 | 4.1 | 0 | Hydrophobic |
| CAI | CD1 | ILE- 185 | 4.29 | 0 | Hydrophobic |
| CAE | CG2 | ILE- 185 | 4 | 0 | Hydrophobic |
