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
2007-01-12
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.700 | 8.700 | 8.700 | 0.000 | 8.700 | 1 |
| 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: | 43.270 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.612 | 664.875 |
| % Hydrophobic | % Polar |
|---|---|
| 40.10 | 59.90 |
| According to VolSite | |
| HET Code: | 82A |
|---|---|
| Formula: | C22H17Cl2FN4O2 |
| Molecular weight: | 459.300 g/mol |
| DrugBank ID: | DB07264 |
| Buried Surface Area: | 65.88 % |
| Polar Surface area: | 93.8 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -13.5275 | 14.1279 | 39.9594 |
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 |
| C26 | CG2 | ILE- 29 | 3.67 | 0 | Hydrophobic |
| CL33 | CZ | TYR- 34 | 3.96 | 0 | Hydrophobic |
| C24 | CB | VAL- 37 | 4.22 | 0 | Hydrophobic |
| CL25 | CG2 | VAL- 37 | 3.64 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 37 | 3.67 | 0 | Hydrophobic |
| C28 | CG2 | VAL- 37 | 4.18 | 0 | Hydrophobic |
| O7 | NZ | LYS- 52 | 2.72 | 170.09 | H-Bond (Protein Donor) |
| C32 | CD | LYS- 52 | 3.91 | 0 | Hydrophobic |
| C34 | CD | LYS- 52 | 3.68 | 0 | Hydrophobic |
| CL33 | CD1 | ILE- 54 | 3.84 | 0 | Hydrophobic |
| N12 | OE1 | GLN- 103 | 2.69 | 163.69 | H-Bond (Ligand Donor) |
| N15 | O | ASP- 104 | 3 | 147.12 | H-Bond (Ligand Donor) |
| N16 | N | MET- 106 | 2.88 | 167.98 | H-Bond (Protein Donor) |
| C21 | CD2 | LEU- 154 | 3.69 | 0 | Hydrophobic |
| C2 | CB | ASP- 165 | 3.69 | 0 | Hydrophobic |
| O7 | O | HOH- 369 | 3 | 179.96 | H-Bond (Protein Donor) |
