sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 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: | 20.949 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.567 | 702.000 |
| % Hydrophobic | % Polar |
|---|---|
| 43.27 | 56.73 |
| According to VolSite | |
| HET Code: | EK9 |
|---|---|
| Formula: | C24H22N4O2 |
| Molecular weight: | 398.457 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.64 % |
| Polar Surface area: | 90.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -13.2224 | 3.412 | 14.0752 |
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 |
| C13 | CD1 | ILE- 29 | 3.9 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 37 | 3.88 | 0 | Hydrophobic |
| C11 | CB | ALA- 50 | 3.88 | 0 | Hydrophobic |
| O2 | NZ | LYS- 52 | 2.75 | 166.86 | H-Bond (Protein Donor) |
| C21 | CG | LYS- 52 | 4.21 | 0 | Hydrophobic |
| C20 | CD | LYS- 52 | 4.36 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 52 | 3.89 | 152.77 | Pi/Cation |
| C22 | CG2 | ILE- 54 | 3.52 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 82 | 4.07 | 0 | Hydrophobic |
| C12 | CB | GLN- 103 | 3.9 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 105 | 3.97 | 0 | Hydrophobic |
| N4 | N | MET- 106 | 3.28 | 167.64 | H-Bond (Protein Donor) |
| C14 | CB | MET- 106 | 4.15 | 0 | Hydrophobic |
| C17 | CD | LYS- 112 | 4.17 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 154 | 3.61 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 154 | 4.14 | 0 | Hydrophobic |
| C1 | CB | ASP- 165 | 4.47 | 0 | Hydrophobic |
| O1 | OD1 | ASP- 165 | 2.68 | 155.07 | H-Bond (Ligand Donor) |
