sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.350 Å
X-ray
2012-05-01
| Name: | Mitogen-activated protein kinase 13 |
|---|---|
| ID: | MK13_HUMAN |
| AC: | O15264 |
| 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: | 30.703 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.232 | 968.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.40 | 44.60 |
| According to VolSite | |
| HET Code: | 0RX |
|---|---|
| Formula: | C21H20N4O3 |
| Molecular weight: | 376.408 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.53 % |
| Polar Surface area: | 76.58 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -13.9461 | 10.4261 | -27.4054 |
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 |
| C11 | CG2 | VAL- 39 | 4.18 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 39 | 3.95 | 0 | Hydrophobic |
| C10 | CB | ALA- 52 | 3.77 | 0 | Hydrophobic |
| C12 | CD | LYS- 54 | 3.33 | 0 | Hydrophobic |
| C19 | CG | ARG- 68 | 3.73 | 0 | Hydrophobic |
| C18 | CG | ARG- 68 | 4.04 | 0 | Hydrophobic |
| C17 | CG | GLU- 72 | 3.63 | 0 | Hydrophobic |
| C21 | CG | GLU- 72 | 3.44 | 0 | Hydrophobic |
| C19 | CB | GLU- 72 | 4.28 | 0 | Hydrophobic |
| N1 | OE1 | GLU- 72 | 2.83 | 169.36 | H-Bond (Ligand Donor) |
| C14 | CD2 | LEU- 76 | 3.48 | 0 | Hydrophobic |
| C14 | CG2 | ILE- 85 | 4.44 | 0 | Hydrophobic |
| C12 | SD | MET- 107 | 3.67 | 0 | Hydrophobic |
| C10 | CE | MET- 107 | 3.99 | 0 | Hydrophobic |
| C11 | CE | MET- 107 | 3.49 | 0 | Hydrophobic |
| N2 | N | MET- 110 | 3.02 | 160.34 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 167 | 3.99 | 0 | Hydrophobic |
| O1 | N | ASP- 168 | 3.12 | 171.97 | H-Bond (Protein Donor) |
| C18 | CD2 | LEU- 171 | 4.12 | 0 | Hydrophobic |
