sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.420 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: | 43.887 |
|---|---|
| Number of residues: | 22 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.021 | 1026.000 |
| % Hydrophobic | % Polar |
|---|---|
| 43.09 | 56.91 |
| According to VolSite | |
| HET Code: | 1BJ |
|---|---|
| Formula: | C17H19N5O |
| Molecular weight: | 309.366 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 51.07 % |
| Polar Surface area: | 75.86 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.27652 | 0.242826 | 12.6747 |
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 |
| C20 | CD1 | ILE- 32 | 4.08 | 0 | Hydrophobic |
| C21 | CG1 | ILE- 32 | 4.44 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 32 | 4.21 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 40 | 4.21 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 40 | 3.63 | 0 | Hydrophobic |
| C5 | CB | ALA- 53 | 3.59 | 0 | Hydrophobic |
| C5 | SD | MET- 108 | 3.99 | 0 | Hydrophobic |
| N1 | N | MET- 111 | 3.05 | 169.71 | H-Bond (Protein Donor) |
| N8 | O | MET- 111 | 2.91 | 138.19 | H-Bond (Ligand Donor) |
| C11 | CB | ASN- 114 | 4.28 | 0 | Hydrophobic |
| C10 | CG1 | VAL- 158 | 3.88 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 168 | 3.65 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 168 | 4.15 | 0 | Hydrophobic |
