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
2006-11-02
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.920 | 8.920 | 8.920 | 0.000 | 8.920 | 1 |
| Name: | Interleukin-1 receptor-associated kinase 4 |
|---|---|
| ID: | IRAK4_HUMAN |
| AC: | Q9NWZ3 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 33.114 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.225 | 941.625 |
| % Hydrophobic | % Polar |
|---|---|
| 45.52 | 54.48 |
| According to VolSite | |
| HET Code: | T12 |
|---|---|
| Formula: | C22H24N4O6 |
| Molecular weight: | 440.449 g/mol |
| DrugBank ID: | DB08590 |
| Buried Surface Area: | 62.43 % |
| Polar Surface area: | 139.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 2.53219 | -7.87575 | 30.5156 |
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 |
| C4 | SD | MET- 192 | 4.23 | 0 | Hydrophobic |
| C39 | CB | MET- 192 | 3.89 | 0 | Hydrophobic |
| C1 | CB | MET- 192 | 3.82 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 200 | 4.21 | 0 | Hydrophobic |
| C39 | CB | VAL- 200 | 4.06 | 0 | Hydrophobic |
| C40 | CG2 | VAL- 200 | 4.24 | 0 | Hydrophobic |
| C15 | CB | ALA- 211 | 3.56 | 0 | Hydrophobic |
| O56 | NZ | LYS- 213 | 3.24 | 148.45 | H-Bond (Protein Donor) |
| O56 | NZ | LYS- 213 | 3.24 | 0 | Ionic (Protein Cationic) |
| O55 | NZ | LYS- 213 | 3.89 | 0 | Ionic (Protein Cationic) |
| C11 | CG1 | VAL- 246 | 3.86 | 0 | Hydrophobic |
| C12 | CG | TYR- 262 | 3.29 | 0 | Hydrophobic |
| C11 | CB | TYR- 262 | 3.26 | 0 | Hydrophobic |
| O53 | N | MET- 265 | 2.8 | 164.06 | H-Bond (Protein Donor) |
| C10 | CG | MET- 265 | 3.54 | 0 | Hydrophobic |
| C43 | CB | SER- 269 | 4.05 | 0 | Hydrophobic |
| C31 | CB | ASP- 278 | 4.37 | 0 | Hydrophobic |
| C35 | CG2 | THR- 280 | 3.82 | 0 | Hydrophobic |
| C31 | CG2 | THR- 280 | 3.92 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 318 | 3.24 | 0 | Hydrophobic |
| O56 | O | HOH- 636 | 2.89 | 154.38 | H-Bond (Protein Donor) |
| O46 | O | HOH- 669 | 3.07 | 147.07 | H-Bond (Protein Donor) |
