sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1998-06-08
| 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: | 19.110 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.218 | 502.875 |
| % Hydrophobic | % Polar |
|---|---|
| 61.07 | 38.93 |
| According to VolSite | |
| HET Code: | SB2 |
|---|---|
| Formula: | C21H16FN3OS |
| Molecular weight: | 377.435 g/mol |
| DrugBank ID: | DB08521 |
| Buried Surface Area: | 59.67 % |
| Polar Surface area: | 77.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -12.9756 | 13.1955 | 40.5616 |
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 |
| CA1 | CG2 | VAL- 39 | 4.46 | 0 | Hydrophobic |
| CD1 | CG1 | VAL- 39 | 4.48 | 0 | Hydrophobic |
| CB5 | CG1 | VAL- 39 | 4.13 | 0 | Hydrophobic |
| CD1 | CB | ALA- 52 | 4.27 | 0 | Hydrophobic |
| CB5 | CB | ALA- 52 | 3.75 | 0 | Hydrophobic |
| CD5 | CD | LYS- 54 | 4.39 | 0 | Hydrophobic |
| CD1 | CB | LYS- 54 | 3.76 | 0 | Hydrophobic |
| CB3 | CG1 | ILE- 84 | 4.4 | 0 | Hydrophobic |
| CD4 | CG2 | ILE- 84 | 4.2 | 0 | Hydrophobic |
| FD3 | CG1 | ILE- 86 | 4.37 | 0 | Hydrophobic |
| FD3 | CB | LEU- 103 | 3.27 | 0 | Hydrophobic |
| CB3 | CG2 | THR- 105 | 3.75 | 0 | Hydrophobic |
| CD3 | CG2 | THR- 105 | 3.5 | 0 | Hydrophobic |
| NB1 | N | MET- 108 | 2.84 | 142.76 | H-Bond (Protein Donor) |
| C1 | CD | LYS- 151 | 4.23 | 0 | Hydrophobic |
| C1 | CB | SER- 153 | 4.17 | 0 | Hydrophobic |
| CA5 | CD2 | LEU- 156 | 4.46 | 0 | Hydrophobic |
| CB3 | CD1 | LEU- 156 | 3.37 | 0 | Hydrophobic |
| CA5 | SG | CYS- 166 | 3.38 | 0 | Hydrophobic |
