sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.830 Å
X-ray
2013-05-02
| Name: | Inhibitor of nuclear factor kappa-B kinase subunit beta |
|---|---|
| ID: | IKKB_HUMAN |
| AC: | O14920 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.11.10 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 41.971 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.958 | 614.250 |
| % Hydrophobic | % Polar |
|---|---|
| 47.80 | 52.20 |
| According to VolSite | |
| HET Code: | KSA |
|---|---|
| Formula: | C27H21N3O5 |
| Molecular weight: | 467.473 g/mol |
| DrugBank ID: | DB02152 |
| Buried Surface Area: | 66.64 % |
| Polar Surface area: | 94.72 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 8 |
| Aromatic rings: | 5 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -13.7581 | -32.0945 | -73.6135 |
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 |
| C24 | CB | LEU- 21 | 4.16 | 0 | Hydrophobic |
| C4 | CB | LEU- 21 | 3.8 | 0 | Hydrophobic |
| C17 | CB | LEU- 21 | 3.83 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 21 | 4.25 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 21 | 3.87 | 0 | Hydrophobic |
| C26 | CG2 | THR- 23 | 4.02 | 0 | Hydrophobic |
| C25 | CG2 | VAL- 29 | 3.82 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 29 | 3.92 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 29 | 3.68 | 0 | Hydrophobic |
| C7 | CB | ALA- 42 | 4.16 | 0 | Hydrophobic |
| C12 | CD | LYS- 44 | 3.68 | 0 | Hydrophobic |
| C14 | SD | MET- 96 | 3.59 | 0 | Hydrophobic |
| N3 | O | GLU- 97 | 2.72 | 164.25 | H-Bond (Ligand Donor) |
| C21 | CE2 | TYR- 98 | 3.47 | 0 | Hydrophobic |
| O2 | N | CYS- 99 | 2.7 | 172.26 | H-Bond (Protein Donor) |
| C27 | CB | ASP- 103 | 4.2 | 0 | Hydrophobic |
| C26 | CB | GLU- 149 | 3.78 | 0 | Hydrophobic |
| O4 | O | GLU- 149 | 2.57 | 164.05 | H-Bond (Ligand Donor) |
| C16 | CG1 | VAL- 152 | 3.84 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 152 | 3.82 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 165 | 4.05 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 165 | 4.17 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 165 | 3.61 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 165 | 3.55 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 165 | 3.55 | 0 | Hydrophobic |
| C14 | CB | ILE- 165 | 3.72 | 0 | Hydrophobic |
| C12 | CB | ASP- 166 | 3.39 | 0 | Hydrophobic |
