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
2008-08-20
| Name: | Dual specificity mitogen-activated protein kinase kinase 1 |
|---|---|
| ID: | MP2K1_HUMAN |
| AC: | Q02750 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.12.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 46.126 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 1 |
| Cofactors: | ATP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.120 | 1397.250 |
| % Hydrophobic | % Polar |
|---|---|
| 41.06 | 58.94 |
| According to VolSite | |
| HET Code: | VRA |
|---|---|
| Formula: | C19H20F3IN2O5S |
| Molecular weight: | 572.337 g/mol |
| DrugBank ID: | DB06309 |
| Buried Surface Area: | 68.81 % |
| Polar Surface area: | 116.27 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 31.1239 | 28.1838 | 39.8953 |
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 |
| F15 | CD | LYS- 97 | 3.42 | 0 | Hydrophobic |
| O21 | NZ | LYS- 97 | 2.9 | 136.71 | H-Bond (Protein Donor) |
| C23 | CD1 | ILE- 99 | 3.76 | 0 | Hydrophobic |
| F16 | CD2 | LEU- 115 | 3.26 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 118 | 4.32 | 0 | Hydrophobic |
| F16 | CD2 | LEU- 118 | 4.3 | 0 | Hydrophobic |
| I14 | CB | VAL- 127 | 3.92 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 141 | 4.27 | 0 | Hydrophobic |
| F16 | CD1 | ILE- 141 | 3.86 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 141 | 3.71 | 0 | Hydrophobic |
| C6 | SD | MET- 143 | 3.82 | 0 | Hydrophobic |
| F15 | CE | MET- 143 | 3.76 | 0 | Hydrophobic |
| O28 | OD1 | ASP- 190 | 2.83 | 152.14 | H-Bond (Ligand Donor) |
| C2 | CB | ASP- 208 | 4.46 | 0 | Hydrophobic |
| I14 | CE2 | PHE- 209 | 4.29 | 0 | Hydrophobic |
| F17 | CG1 | VAL- 211 | 3.2 | 0 | Hydrophobic |
| F17 | CB | SER- 212 | 3.32 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 215 | 4.21 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 215 | 3.54 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 216 | 4.43 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 216 | 4.3 | 0 | Hydrophobic |
| C23 | SD | MET- 219 | 3.7 | 0 | Hydrophobic |
| C31 | CG | MET- 219 | 3.99 | 0 | Hydrophobic |
| C25 | CE | MET- 219 | 3.76 | 0 | Hydrophobic |
| O29 | O3G | ATP- 600 | 3.1 | 160.55 | H-Bond (Ligand Donor) |
| N18 | O | HOH- 1022 | 2.8 | 139.37 | H-Bond (Ligand Donor) |
