sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2012-06-29
| 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: | 34.737 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.861 | 472.500 |
| % Hydrophobic | % Polar |
|---|---|
| 47.86 | 52.14 |
| According to VolSite | |
| HET Code: | EK7 |
|---|---|
| Formula: | C19H17N5OS |
| Molecular weight: | 363.436 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 57.43 % |
| Polar Surface area: | 113.31 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| 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 |
|---|---|---|
| -16.8951 | 2.88012 | 15.9602 |
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 |
| C17 | CG2 | ILE- 29 | 3.57 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 29 | 3.56 | 0 | Hydrophobic |
| C17 | CG1 | VAL- 37 | 3.81 | 0 | Hydrophobic |
| S | CG2 | VAL- 37 | 4.24 | 0 | Hydrophobic |
| C7 | CB | ALA- 50 | 3.71 | 0 | Hydrophobic |
| N5 | NZ | LYS- 52 | 3.45 | 177.41 | H-Bond (Protein Donor) |
| C8 | CB | GLN- 103 | 4.39 | 0 | Hydrophobic |
| N2 | N | MET- 106 | 3.05 | 162.86 | H-Bond (Protein Donor) |
| N3 | O | MET- 106 | 2.89 | 149.76 | H-Bond (Ligand Donor) |
| C13 | CD | LYS- 112 | 3.67 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 154 | 4.33 | 0 | Hydrophobic |
| C15 | CD2 | LEU- 154 | 4.34 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 154 | 3.61 | 0 | Hydrophobic |
| C9 | SG | CYS- 164 | 4.1 | 0 | Hydrophobic |
