sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2012-11-14
| Name: | Mitogen-activated protein kinase 8 |
|---|---|
| ID: | MK08_HUMAN |
| AC: | P45983 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.24 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.677 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.818 | 634.500 |
| % Hydrophobic | % Polar |
|---|---|
| 49.47 | 50.53 |
| According to VolSite | |
| HET Code: | 1BK |
|---|---|
| Formula: | C21H27N5O4S |
| Molecular weight: | 445.535 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 53.16 % |
| Polar Surface area: | 127.61 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -2.24971 | 0.73371 | 13.7931 |
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 |
| C15 | CG1 | ILE- 32 | 4.16 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 32 | 3.76 | 0 | Hydrophobic |
| C17 | CD1 | ILE- 32 | 3.97 | 0 | Hydrophobic |
| C29 | CB | GLN- 37 | 4.27 | 0 | Hydrophobic |
| O31 | N | GLN- 37 | 2.89 | 145.26 | H-Bond (Protein Donor) |
| O31 | N | GLY- 38 | 3.4 | 121.2 | H-Bond (Protein Donor) |
| C14 | CB | VAL- 40 | 4.43 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 40 | 3.81 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 40 | 3.65 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 40 | 3.81 | 0 | Hydrophobic |
| C5 | CB | ALA- 53 | 3.65 | 0 | Hydrophobic |
| C5 | SD | MET- 108 | 4.18 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 110 | 4.42 | 0 | Hydrophobic |
| N1 | O | MET- 111 | 2.87 | 159.1 | H-Bond (Ligand Donor) |
| N3 | N | MET- 111 | 3.04 | 161.97 | H-Bond (Protein Donor) |
| C18 | CG1 | VAL- 158 | 4 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 168 | 3.62 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 168 | 4.11 | 0 | Hydrophobic |
