sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2012-07-24
| 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 |
|---|---|
| B | 100 % |
| B-Factor: | 32.964 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | ATP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.010 | 597.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.54 | 47.46 |
| According to VolSite | |
| HET Code: | 4BM |
|---|---|
| Formula: | C16H14F3IN2O4 |
| Molecular weight: | 482.193 g/mol |
| DrugBank ID: | DB07101 |
| Buried Surface Area: | 74.17 % |
| 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 |
|---|---|---|
| 68.368 | 107.278 | -31.4318 |
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 |
| O16 | NZ | LYS- 97 | 2.88 | 156.21 | H-Bond (Protein Donor) |
| C20 | CD | LYS- 97 | 3.84 | 0 | Hydrophobic |
| F24 | CD | LYS- 97 | 3.58 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 99 | 3.97 | 0 | Hydrophobic |
| F25 | CD2 | LEU- 115 | 3.32 | 0 | Hydrophobic |
| C02 | CD1 | LEU- 118 | 4.22 | 0 | Hydrophobic |
| C03 | CD2 | LEU- 118 | 3.82 | 0 | Hydrophobic |
| C04 | CD1 | LEU- 118 | 4.18 | 0 | Hydrophobic |
| F25 | CD1 | LEU- 118 | 4.28 | 0 | Hydrophobic |
| I23 | CB | VAL- 127 | 4.12 | 0 | Hydrophobic |
| C01 | CD1 | ILE- 141 | 4.25 | 0 | Hydrophobic |
| C08 | CD1 | ILE- 141 | 4.46 | 0 | Hydrophobic |
| F24 | CG2 | ILE- 141 | 3.49 | 0 | Hydrophobic |
| I23 | CG | MET- 143 | 4.34 | 0 | Hydrophobic |
| F24 | CE | MET- 143 | 4.17 | 0 | Hydrophobic |
| C05 | SD | MET- 143 | 3.67 | 0 | Hydrophobic |
| C01 | CB | ASP- 208 | 4.46 | 0 | Hydrophobic |
| C09 | CB | ASP- 208 | 4.38 | 0 | Hydrophobic |
| I23 | CE2 | PHE- 209 | 3.96 | 0 | Hydrophobic |
| C13 | CG2 | VAL- 211 | 4.23 | 0 | Hydrophobic |
| F26 | CG2 | VAL- 211 | 3.76 | 0 | Hydrophobic |
| F26 | CB | SER- 212 | 3.71 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 215 | 3.65 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 215 | 3.65 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 216 | 4.11 | 0 | Hydrophobic |
| F26 | CG1 | ILE- 216 | 4.41 | 0 | Hydrophobic |
| C19 | CE | MET- 219 | 4.48 | 0 | Hydrophobic |
| C10 | CE | MET- 219 | 3.54 | 0 | Hydrophobic |
| O21 | O3G | ATP- 502 | 3.01 | 132.63 | H-Bond (Ligand Donor) |
