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
2006-08-16
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.570 | 6.920 | 6.920 | 0.360 | 7.300 | 4 |
| 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: | 31.266 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.287 | 590.625 |
| % Hydrophobic | % Polar |
|---|---|
| 61.71 | 38.29 |
| According to VolSite | |
| HET Code: | LY4 |
|---|---|
| Formula: | C28H29N4O3 |
| Molecular weight: | 469.555 g/mol |
| DrugBank ID: | DB11829 |
| Buried Surface Area: | 62.53 % |
| Polar Surface area: | 69.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 42.2167 | -1.92554 | -0.102171 |
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 |
| CBB | CB | LEU- 44 | 4.42 | 0 | Hydrophobic |
| CAJ | CD1 | LEU- 44 | 3.66 | 0 | Hydrophobic |
| CAI | CD2 | LEU- 44 | 3.52 | 0 | Hydrophobic |
| CBD | CZ | PHE- 49 | 3.7 | 0 | Hydrophobic |
| CBB | CE1 | PHE- 49 | 4.03 | 0 | Hydrophobic |
| CAZ | CB | PHE- 49 | 3.96 | 0 | Hydrophobic |
| CBB | CB | VAL- 52 | 3.95 | 0 | Hydrophobic |
| CAN | CG1 | VAL- 52 | 4.23 | 0 | Hydrophobic |
| CAX | CG2 | VAL- 52 | 3.64 | 0 | Hydrophobic |
| CAP | CD | LYS- 67 | 4.46 | 0 | Hydrophobic |
| NAD | O | GLU- 121 | 2.8 | 169.13 | H-Bond (Ligand Donor) |
| CAJ | CD | ARG- 122 | 3.74 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 126 | 3.31 | 0 | Hydrophobic |
| CBA | CB | ASP- 128 | 3.98 | 0 | Hydrophobic |
| CAK | CD1 | LEU- 174 | 4.43 | 0 | Hydrophobic |
| CAS | CD2 | LEU- 174 | 4.27 | 0 | Hydrophobic |
| CBA | CD2 | LEU- 174 | 3.53 | 0 | Hydrophobic |
| CAN | CD1 | ILE- 185 | 4.01 | 0 | Hydrophobic |
| CAO | CB | ILE- 185 | 3.79 | 0 | Hydrophobic |
| CAZ | CB | ASP- 186 | 3.88 | 0 | Hydrophobic |
