sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2009-09-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.300 | 8.300 | 8.300 | 0.000 | 8.300 | 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: | 27.724 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.015 | 718.875 |
| % Hydrophobic | % Polar |
|---|---|
| 53.05 | 46.95 |
| According to VolSite | |
| HET Code: | LYG |
|---|---|
| Formula: | C15H15ClN3O2S |
| Molecular weight: | 336.816 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 55.8 % |
| Polar Surface area: | 94.37 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -40.2201 | -3.04955 | 0.655773 |
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 |
| CL1 | CD2 | LEU- 44 | 3.71 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 52 | 4.28 | 0 | Hydrophobic |
| C10 | CB | ALA- 65 | 3.45 | 0 | Hydrophobic |
| O2 | NZ | LYS- 67 | 2.68 | 155.32 | H-Bond (Protein Donor) |
| S1 | CG2 | ILE- 104 | 4.35 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 104 | 3.78 | 0 | Hydrophobic |
| S1 | CD1 | LEU- 120 | 3.9 | 0 | Hydrophobic |
| CL1 | CD | ARG- 122 | 4 | 0 | Hydrophobic |
| C10 | CB | ARG- 122 | 4.22 | 0 | Hydrophobic |
| CL1 | CG1 | VAL- 126 | 4.29 | 0 | Hydrophobic |
| C1 | CB | GLU- 171 | 4.25 | 0 | Hydrophobic |
| O1 | OD1 | ASN- 172 | 2.78 | 162.86 | H-Bond (Ligand Donor) |
| C8 | CD1 | LEU- 174 | 4.08 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 174 | 3.51 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 185 | 4.22 | 0 | Hydrophobic |
| S1 | CG2 | ILE- 185 | 3.73 | 0 | Hydrophobic |
| N1 | OD2 | ASP- 186 | 3.7 | 0 | Ionic (Ligand Cationic) |
