sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 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: | 31.967 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.288 | 1009.125 |
| % Hydrophobic | % Polar |
|---|---|
| 59.87 | 40.13 |
| According to VolSite | |
| HET Code: | N61 |
|---|---|
| Formula: | C20H23N5O2 |
| Molecular weight: | 365.429 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.93 % |
| Polar Surface area: | 81.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -12.9576 | 12.2101 | -27.7893 |
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 |
| C12 | CG2 | VAL- 39 | 3.79 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 39 | 4.05 | 0 | Hydrophobic |
| C15 | CB | ALA- 52 | 3.8 | 0 | Hydrophobic |
| C12 | CB | LYS- 54 | 4.25 | 0 | Hydrophobic |
| C11 | CD | LYS- 54 | 3.87 | 0 | Hydrophobic |
| N3 | OE1 | GLU- 72 | 2.92 | 138.56 | H-Bond (Ligand Donor) |
| N4 | OE1 | GLU- 72 | 2.88 | 142.5 | H-Bond (Ligand Donor) |
| C1 | CG | GLU- 72 | 3.81 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 75 | 4.2 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 76 | 4.41 | 0 | Hydrophobic |
| C4 | CG | MET- 79 | 3.89 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 84 | 4.32 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 84 | 3.61 | 0 | Hydrophobic |
| C11 | SD | MET- 107 | 3.5 | 0 | Hydrophobic |
| C15 | CE | MET- 107 | 4.26 | 0 | Hydrophobic |
| C12 | CE | MET- 107 | 3.45 | 0 | Hydrophobic |
| N5 | N | MET- 110 | 2.9 | 155.92 | H-Bond (Protein Donor) |
| C5 | CG1 | VAL- 146 | 4.43 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 166 | 3.86 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 167 | 3.69 | 0 | Hydrophobic |
| O1 | N | ASP- 168 | 2.98 | 174.2 | H-Bond (Protein Donor) |
| C6 | CB | ASP- 168 | 4.48 | 0 | Hydrophobic |
| C1 | CB | ASP- 168 | 3.96 | 0 | Hydrophobic |
| C19 | CE1 | PHE- 169 | 3.3 | 0 | Hydrophobic |
