sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2012-01-05
| Name: | Dual specificity mitogen-activated protein kinase kinase 6 |
|---|---|
| ID: | MP2K6_HUMAN |
| AC: | P52564 |
| 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: | 86.552 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.318 | 735.750 |
| % Hydrophobic | % Polar |
|---|---|
| 40.37 | 59.63 |
| According to VolSite | |
| HET Code: | ANK |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.23 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -6.33187 | -33.4754 | 2.09639 |
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 |
| C1' | CG1 | VAL- 67 | 3.68 | 0 | Hydrophobic |
| C4' | CG1 | VAL- 67 | 4.05 | 0 | Hydrophobic |
| O2A | NZ | LYS- 82 | 3.45 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 82 | 3.25 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 82 | 3.25 | 129.39 | H-Bond (Protein Donor) |
| N6 | O | GLU- 130 | 2.71 | 144.87 | H-Bond (Ligand Donor) |
| N1 | N | MET- 132 | 2.91 | 136.57 | H-Bond (Protein Donor) |
| C2' | CB | SER- 135 | 4.05 | 0 | Hydrophobic |
| C3' | CD | LYS- 138 | 4.45 | 0 | Hydrophobic |
| O2G | NZ | LYS- 181 | 2.53 | 136.84 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 181 | 2.53 | 0 | Ionic (Protein Cationic) |
| O2G | NZ | LYS- 210 | 3.05 | 144.11 | H-Bond (Protein Donor) |
| O2G | NZ | LYS- 210 | 3.05 | 0 | Ionic (Protein Cationic) |
| O3G | NZ | LYS- 210 | 3.68 | 0 | Ionic (Protein Cationic) |
| O2B | MG | MG- 402 | 2.51 | 0 | Metal Acceptor |
