sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2004-06-30
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.070 | 6.360 | 6.510 | 0.210 | 6.510 | 3 |
| 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: | 28.923 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.770 | 762.750 |
| % Hydrophobic | % Polar |
|---|---|
| 41.15 | 58.85 |
| According to VolSite | |
| HET Code: | FRZ |
|---|---|
| Formula: | C18H13N7 |
| Molecular weight: | 327.343 g/mol |
| DrugBank ID: | DB07794 |
| Buried Surface Area: | 62.87 % |
| Polar Surface area: | 97.77 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 6.42892 | -4.37184 | 16.444 |
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 |
| C15 | CG1 | VAL- 39 | 4.38 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 39 | 3.88 | 0 | Hydrophobic |
| C15 | CB | ALA- 52 | 4.08 | 0 | Hydrophobic |
| C23 | CB | ALA- 52 | 4.14 | 0 | Hydrophobic |
| N7 | NZ | LYS- 54 | 3.48 | 146.85 | H-Bond (Protein Donor) |
| C11 | CD | LYS- 54 | 3.98 | 0 | Hydrophobic |
| C15 | CB | LYS- 54 | 3.52 | 0 | Hydrophobic |
| C13 | CB | ILE- 103 | 3.88 | 0 | Hydrophobic |
| N30 | OE1 | GLN- 105 | 3.22 | 146.88 | H-Bond (Ligand Donor) |
| C14 | CG | GLN- 105 | 3.61 | 0 | Hydrophobic |
| N30 | O | ASP- 106 | 3.03 | 159.31 | H-Bond (Ligand Donor) |
| N28 | N | MET- 108 | 2.99 | 154.6 | H-Bond (Protein Donor) |
| C22 | CD2 | LEU- 156 | 3.72 | 0 | Hydrophobic |
| C23 | CG | LEU- 156 | 3.75 | 0 | Hydrophobic |
