sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2011-06-09
| Name: | Proteasome subunit beta type-5 | Proteasome subunit beta type-6 |
|---|---|---|
| ID: | PSB5_YEAST | PSB6_YEAST |
| AC: | P30656 | P23724 |
| Organism: | Saccharomyces cerevisiae | |
| Reign: | Eukaryota | |
| TaxID: | 559292 | |
| EC Number: | 3.4.25.1 | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| K | 64 % |
| L | 36 % |
| B-Factor: | 40.729 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.146 | 924.750 |
| % Hydrophobic | % Polar |
|---|---|
| 44.53 | 55.47 |
| According to VolSite | |
| HET Code: | P3N |
|---|---|
| Formula: | C32H38N6O5 |
| Molecular weight: | 586.681 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 44.47 % |
| Polar Surface area: | 152.25 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 10.853 | -136.606 | 19.3808 |
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 |
| C17 | CB | ALA- 20 | 4.02 | 0 | Hydrophobic |
| N8 | O | THR- 21 | 2.72 | 158.73 | H-Bond (Ligand Donor) |
| O14 | N | THR- 21 | 3.09 | 147.15 | H-Bond (Protein Donor) |
| C43 | CB | ALA- 22 | 4.32 | 0 | Hydrophobic |
| C18 | CG1 | VAL- 31 | 3.33 | 0 | Hydrophobic |
| C20 | CG | LYS- 33 | 3.9 | 0 | Hydrophobic |
| C22 | SD | MET- 45 | 3.81 | 0 | Hydrophobic |
| C20 | CB | MET- 45 | 3.72 | 0 | Hydrophobic |
| N11 | O | GLY- 47 | 2.73 | 166.32 | H-Bond (Ligand Donor) |
| C2 | CB | ALA- 49 | 4.31 | 0 | Hydrophobic |
| C17 | CB | ALA- 49 | 3.74 | 0 | Hydrophobic |
| C18 | CB | ALA- 49 | 3.59 | 0 | Hydrophobic |
| O6 | N | ALA- 49 | 3.07 | 167.43 | H-Bond (Protein Donor) |
| C25 | CB | SER- 96 | 3.86 | 0 | Hydrophobic |
| C41 | CB | HIS- 98 | 4.12 | 0 | Hydrophobic |
| C41 | CB | ASP- 114 | 4.15 | 0 | Hydrophobic |
| C2 | CB | ASP- 114 | 4.16 | 0 | Hydrophobic |
| N4 | OD1 | ASP- 114 | 3.32 | 159.65 | H-Bond (Ligand Donor) |
| C35 | CB | PRO- 115 | 4.48 | 0 | Hydrophobic |
