sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2012-03-15
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.510 | 8.460 | 8.460 | 0.940 | 9.400 | 2 |
| 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: | 40.914 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ATP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.149 | 847.125 |
| % Hydrophobic | % Polar |
|---|---|
| 54.58 | 45.42 |
| According to VolSite | |
| HET Code: | 5Y0 |
|---|---|
| Formula: | C16H14F3IN2O4 |
| Molecular weight: | 482.193 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.97 % |
| Polar Surface area: | 90.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 4.78608 | 34.478 | 4.99642 |
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 |
| O26 | N | GLY- 79 | 3.49 | 150.01 | H-Bond (Protein Donor) |
| O11 | NZ | LYS- 97 | 2.78 | 130.12 | H-Bond (Protein Donor) |
| F19 | CD | LYS- 97 | 4.23 | 0 | Hydrophobic |
| F7 | CD2 | LEU- 115 | 3.61 | 0 | Hydrophobic |
| I20 | CD1 | LEU- 118 | 4.49 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 118 | 3.83 | 0 | Hydrophobic |
| I20 | CB | VAL- 127 | 4.21 | 0 | Hydrophobic |
| C13 | CD1 | ILE- 141 | 4.17 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 141 | 4.45 | 0 | Hydrophobic |
| F19 | CG2 | ILE- 141 | 3.47 | 0 | Hydrophobic |
| C17 | SD | MET- 143 | 3.73 | 0 | Hydrophobic |
| I20 | CB | CYS- 207 | 4.45 | 0 | Hydrophobic |
| C16 | CB | CYS- 207 | 4.36 | 0 | Hydrophobic |
| C6 | CB | ASP- 208 | 4.26 | 0 | Hydrophobic |
| I20 | CZ | PHE- 209 | 4.34 | 0 | Hydrophobic |
| C14 | CG2 | VAL- 211 | 4.5 | 0 | Hydrophobic |
| F7 | CG2 | VAL- 211 | 3.46 | 0 | Hydrophobic |
| F8 | CG2 | VAL- 211 | 3.89 | 0 | Hydrophobic |
| F8 | CB | SER- 212 | 3.96 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 215 | 3.64 | 0 | Hydrophobic |
| C3 | CD1 | LEU- 215 | 3.64 | 0 | Hydrophobic |
| C24 | CE | MET- 219 | 4.1 | 0 | Hydrophobic |
| O26 | O1G | ATP- 1383 | 2.82 | 133.63 | H-Bond (Ligand Donor) |
