sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2013-01-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.850 | 9.850 | 9.850 | 0.000 | 9.850 | 1 |
| Name: | Mitogen-activated protein kinase 8 |
|---|---|
| ID: | MK08_HUMAN |
| AC: | P45983 |
| 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: | 47.039 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.939 | 526.500 |
| % Hydrophobic | % Polar |
|---|---|
| 53.21 | 46.79 |
| According to VolSite | |
| HET Code: | 1J2 |
|---|---|
| Formula: | C24H31N5O3S |
| Molecular weight: | 469.600 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 54.11 % |
| Polar Surface area: | 108.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| -12.961 | 6.37473 | -21.2683 |
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 |
| C12 | CD1 | ILE- 32 | 3.83 | 0 | Hydrophobic |
| C13 | CG1 | ILE- 32 | 4.04 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 32 | 4.22 | 0 | Hydrophobic |
| O32 | N | GLN- 37 | 2.9 | 154.15 | H-Bond (Protein Donor) |
| C33 | CB | GLN- 37 | 4.12 | 0 | Hydrophobic |
| O32 | N | GLY- 38 | 3.37 | 130.34 | H-Bond (Protein Donor) |
| C15 | CG2 | VAL- 40 | 3.63 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 40 | 3.87 | 0 | Hydrophobic |
| C14 | CB | VAL- 40 | 4.17 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 40 | 4.06 | 0 | Hydrophobic |
| C5 | CB | ALA- 53 | 3.7 | 0 | Hydrophobic |
| O31 | NZ | LYS- 55 | 2.93 | 148.54 | H-Bond (Protein Donor) |
| C5 | CD1 | ILE- 86 | 4.24 | 0 | Hydrophobic |
| C5 | SD | MET- 108 | 4.2 | 0 | Hydrophobic |
| N1 | N | MET- 111 | 2.93 | 156.43 | H-Bond (Protein Donor) |
| N17 | O | MET- 111 | 2.85 | 171.73 | H-Bond (Ligand Donor) |
| C20 | CB | ASN- 114 | 4.44 | 0 | Hydrophobic |
| C19 | CG1 | VAL- 158 | 3.85 | 0 | Hydrophobic |
| C5 | CD2 | LEU- 168 | 3.68 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 168 | 4.28 | 0 | Hydrophobic |
