sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
3.000 Å
X-ray
2013-01-21
| 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: | 32.882 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.982 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.92 | 53.08 |
| According to VolSite | |
| HET Code: | 1FM |
|---|---|
| Formula: | C19H21O7 |
| Molecular weight: | 361.366 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.18 % |
| Polar Surface area: | 116.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 1 |
| X | Y | Z |
|---|---|---|
| 15.4824 | 38.6158 | 44.4258 |
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 |
| C3 | CG1 | ILE- 31 | 4.32 | 0 | Hydrophobic |
| C59 | CG2 | ILE- 31 | 3.8 | 0 | Hydrophobic |
| C14 | CB | ILE- 31 | 3.84 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 31 | 4.43 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 39 | 4.34 | 0 | Hydrophobic |
| C18 | CG2 | VAL- 39 | 4.39 | 0 | Hydrophobic |
| C34 | CG2 | VAL- 39 | 4.47 | 0 | Hydrophobic |
| C62 | CG1 | VAL- 39 | 3.85 | 0 | Hydrophobic |
| C62 | CB | ALA- 52 | 4.44 | 0 | Hydrophobic |
| C62 | CB | LYS- 54 | 3.76 | 0 | Hydrophobic |
| O46 | N | MET- 108 | 2.79 | 136.86 | H-Bond (Protein Donor) |
| C11 | CB | MET- 108 | 4.08 | 0 | Hydrophobic |
| O48 | NZ | LYS- 114 | 3.16 | 150.64 | H-Bond (Protein Donor) |
| C2 | CD1 | LEU- 156 | 4.31 | 0 | Hydrophobic |
| C11 | CG | LEU- 156 | 4.46 | 0 | Hydrophobic |
| C31 | SG | CYS- 166 | 3.56 | 0 | Hydrophobic |
| C42 | CB | CYS- 166 | 4.07 | 0 | Hydrophobic |
| C41 | CB | ASP- 167 | 4.07 | 0 | Hydrophobic |
