sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2004-11-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.000 | 8.000 | 8.000 | 0.000 | 8.000 | 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: | 32.428 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.617 | 546.750 |
| % Hydrophobic | % Polar |
|---|---|
| 64.20 | 35.80 |
| According to VolSite | |
| HET Code: | BI1 |
|---|---|
| Formula: | C25H25N4O2 |
| Molecular weight: | 413.492 g/mol |
| DrugBank ID: | DB03777 |
| Buried Surface Area: | 64.19 % |
| Polar Surface area: | 71.33 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -18.4554 | -37.0573 | 0.144645 |
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 |
| CAM | CD1 | LEU- 44 | 4.18 | 0 | Hydrophobic |
| CAS | CB | LEU- 44 | 3.63 | 0 | Hydrophobic |
| CBA | CZ | PHE- 49 | 3.85 | 0 | Hydrophobic |
| CAY | CD1 | PHE- 49 | 4.32 | 0 | Hydrophobic |
| CAF | CB | PHE- 49 | 3.53 | 0 | Hydrophobic |
| CAQ | CB | VAL- 52 | 3.85 | 0 | Hydrophobic |
| CAD | CG2 | VAL- 52 | 4.32 | 0 | Hydrophobic |
| CAP | CG1 | VAL- 52 | 3.75 | 0 | Hydrophobic |
| CAB | CD | LYS- 67 | 3.68 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 120 | 3.53 | 0 | Hydrophobic |
| NAU | O | GLU- 121 | 2.88 | 158.42 | H-Bond (Ligand Donor) |
| CAE | CD1 | ILE- 185 | 4.34 | 0 | Hydrophobic |
| CAD | CB | ILE- 185 | 4.27 | 0 | Hydrophobic |
| CAY | CD1 | ILE- 185 | 3.58 | 0 | Hydrophobic |
| CAY | CB | ASP- 186 | 4.49 | 0 | Hydrophobic |
| CAF | CB | ASP- 186 | 3.46 | 0 | Hydrophobic |
