sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.850 Å
X-ray
2010-08-13
| 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 | 71 % |
| L | 29 % |
| B-Factor: | 42.443 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.393 | 1177.875 |
| % Hydrophobic | % Polar |
|---|---|
| 46.13 | 53.87 |
| According to VolSite | |
| HET Code: | 3OE |
|---|---|
| Formula: | C34H37N3O5S |
| Molecular weight: | 599.740 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 46.64 % |
| Polar Surface area: | 145 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: | 2 |
| Rotatable Bonds: | 14 |
| X | Y | Z |
|---|---|---|
| 12.1533 | -136.748 | 20.0493 |
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 |
| C43 | CB | ALA- 20 | 3.77 | 0 | Hydrophobic |
| S3 | CB | ALA- 20 | 4.27 | 0 | Hydrophobic |
| N13 | O | THR- 21 | 2.99 | 158.71 | H-Bond (Ligand Donor) |
| O10 | N | THR- 21 | 3.11 | 153.81 | H-Bond (Protein Donor) |
| S3 | CG1 | VAL- 31 | 3.24 | 0 | Hydrophobic |
| S3 | CG | LYS- 33 | 4.45 | 0 | Hydrophobic |
| C7 | CB | MET- 45 | 3.46 | 0 | Hydrophobic |
| N29 | O | GLY- 47 | 3 | 163 | H-Bond (Ligand Donor) |
| O16 | N | ALA- 49 | 3.13 | 162.7 | H-Bond (Protein Donor) |
| S3 | CB | ALA- 49 | 3.67 | 0 | Hydrophobic |
| C43 | CB | ALA- 49 | 3.81 | 0 | Hydrophobic |
| C7 | SG | CYS- 52 | 4.08 | 0 | Hydrophobic |
| C38 | CB | PRO- 94 | 3.72 | 0 | Hydrophobic |
| C39 | CG | PRO- 94 | 3.83 | 0 | Hydrophobic |
| C25 | CB | SER- 96 | 4 | 0 | Hydrophobic |
| C36 | CE1 | TYR- 96 | 3.98 | 0 | Hydrophobic |
| C38 | CD1 | TYR- 96 | 3.27 | 0 | Hydrophobic |
| C34 | CB | ASP- 114 | 4.45 | 0 | Hydrophobic |
| C19 | CB | ASP- 114 | 4.03 | 0 | Hydrophobic |
| N18 | OD1 | ASP- 114 | 3.39 | 159.31 | H-Bond (Ligand Donor) |
| C36 | CG | PRO- 115 | 4.03 | 0 | Hydrophobic |
| C33 | CG | PRO- 115 | 3.93 | 0 | Hydrophobic |
| C33 | CG2 | VAL- 116 | 3.92 | 0 | Hydrophobic |
