sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.200 Å
X-ray
2009-07-06
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.170 | 6.170 | 6.170 | 0.000 | 6.170 | 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: | 18.105 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.944 | 732.375 |
| % Hydrophobic | % Polar |
|---|---|
| 41.47 | 58.53 |
| According to VolSite | |
| HET Code: | Z48 |
|---|---|
| Formula: | C24H23N5O2 |
| Molecular weight: | 413.472 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.5 % |
| Polar Surface area: | 102.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 8.67948 | -3.46758 | 44.8128 |
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 |
| C7 | CD1 | ILE- 29 | 4.23 | 0 | Hydrophobic |
| C11 | CB | ILE- 29 | 3.96 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 37 | 3.79 | 0 | Hydrophobic |
| C2 | CB | ALA- 50 | 3.9 | 0 | Hydrophobic |
| O22 | NZ | LYS- 52 | 2.82 | 151.64 | H-Bond (Protein Donor) |
| C29 | CD | LYS- 52 | 4.41 | 0 | Hydrophobic |
| C30 | CG | LYS- 52 | 4.18 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 54 | 3.64 | 0 | Hydrophobic |
| C1 | CG1 | ILE- 82 | 4.08 | 0 | Hydrophobic |
| C1 | CB | GLN- 103 | 4.2 | 0 | Hydrophobic |
| N4 | N | MET- 106 | 3.07 | 167.97 | H-Bond (Protein Donor) |
| N6 | O | MET- 106 | 2.95 | 167.69 | H-Bond (Ligand Donor) |
| C9 | CB | ASP- 109 | 4.19 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 154 | 3.44 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 154 | 3.72 | 0 | Hydrophobic |
| O27 | OD2 | ASP- 165 | 2.68 | 145.39 | H-Bond (Ligand Donor) |
| N17 | O | HOH- 359 | 2.78 | 155.4 | H-Bond (Ligand Donor) |
