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
2003-02-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.500 | 8.500 | 8.500 | 0.000 | 8.500 | 2 |
| Name: | Serine/threonine-protein kinase Chk1 |
|---|---|
| ID: | CHK1_HUMAN |
| AC: | O14757 |
| 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: | 21.274 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.056 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 52.17 | 47.83 |
| According to VolSite | |
| HET Code: | STU |
|---|---|
| Formula: | C28H27N4O3 |
| Molecular weight: | 467.539 g/mol |
| DrugBank ID: | DB02010 |
| Buried Surface Area: | 66.25 % |
| Polar Surface area: | 74.03 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 4.80403 | 6.35223 | 16.9201 |
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 |
| C25 | CB | LEU- 15 | 4.47 | 0 | Hydrophobic |
| C19 | CB | LEU- 15 | 4.43 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 15 | 4.13 | 0 | Hydrophobic |
| C20 | CB | LEU- 15 | 3.79 | 0 | Hydrophobic |
| C3 | CD2 | LEU- 15 | 3.81 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 15 | 3.87 | 0 | Hydrophobic |
| C26 | CZ | TYR- 20 | 3.66 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 23 | 4.01 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 23 | 4.07 | 0 | Hydrophobic |
| C17 | CG2 | VAL- 23 | 3.63 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 23 | 3.99 | 0 | Hydrophobic |
| C7 | CB | ALA- 36 | 4.19 | 0 | Hydrophobic |
| C15 | CD | LYS- 38 | 3.81 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 84 | 3.85 | 0 | Hydrophobic |
| N1 | O | GLU- 85 | 2.84 | 170.45 | H-Bond (Ligand Donor) |
| O5 | N | CYS- 87 | 2.76 | 165.3 | H-Bond (Protein Donor) |
| C24 | CG | GLU- 91 | 4.14 | 0 | Hydrophobic |
| N4 | OE2 | GLU- 91 | 2.69 | 135.6 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 91 | 2.69 | 0 | Ionic (Ligand Cationic) |
| N4 | O | GLU- 134 | 2.92 | 145.9 | H-Bond (Ligand Donor) |
| C20 | CD2 | LEU- 137 | 4.39 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 137 | 4.22 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 137 | 3.53 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 137 | 3.28 | 0 | Hydrophobic |
| C27 | CB | SER- 147 | 4.19 | 0 | Hydrophobic |
| C27 | CB | ASP- 148 | 4.2 | 0 | Hydrophobic |
| C15 | CB | ASP- 148 | 3.68 | 0 | Hydrophobic |
