sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2012-06-28
| Name: | Mitogen-activated protein kinase 1 |
|---|---|
| ID: | MK01_HUMAN |
| AC: | P28482 |
| 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: | 33.734 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.872 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 46.05 | 53.95 |
| According to VolSite | |
| HET Code: | E75 |
|---|---|
| Formula: | C20H22N4O2 |
| Molecular weight: | 350.414 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.21 % |
| Polar Surface area: | 84.07 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: | 4 |
| X | Y | Z |
|---|---|---|
| 20.434 | 6.24346 | 15.7407 |
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 | ILE- 29 | 3.41 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 29 | 3.7 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 37 | 4.09 | 0 | Hydrophobic |
| C6 | CB | ALA- 50 | 3.71 | 0 | Hydrophobic |
| C16 | CB | ALA- 50 | 3.89 | 0 | Hydrophobic |
| C20 | CD | LYS- 52 | 3.46 | 0 | Hydrophobic |
| C17 | CB | LYS- 52 | 3.57 | 0 | Hydrophobic |
| C18 | CG2 | ILE- 101 | 3.84 | 0 | Hydrophobic |
| C17 | CB | GLN- 103 | 4.06 | 0 | Hydrophobic |
| C18 | CG | GLN- 103 | 3.59 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 105 | 4.33 | 0 | Hydrophobic |
| N4 | O | MET- 106 | 2.92 | 159.91 | H-Bond (Ligand Donor) |
| N3 | N | MET- 106 | 3.09 | 164.11 | H-Bond (Protein Donor) |
| C6 | CD1 | LEU- 154 | 3.75 | 0 | Hydrophobic |
