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
1998-05-29
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 7.720 | 7.720 | 0.000 | 7.720 | 1 |
| Name: | ATP-dependent molecular chaperone HSP82 |
|---|---|
| ID: | HSP82_YEAST |
| AC: | P02829 |
| Organism: | Saccharomyces cerevisiae |
| Reign: | Eukaryota |
| TaxID: | 559292 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 15.014 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.853 | 438.750 |
| % Hydrophobic | % Polar |
|---|---|
| 48.46 | 51.54 |
| According to VolSite | |
| HET Code: | RDC |
|---|---|
| Formula: | C18H16ClO6 |
| Molecular weight: | 363.769 g/mol |
| DrugBank ID: | DB03758 |
| Buried Surface Area: | 63.05 % |
| Polar Surface area: | 99.19 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| 16.8143 | -3.28892 | -5.20068 |
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 |
| CL1 | CB | ASN- 37 | 4.45 | 0 | Hydrophobic |
| C5 | CB | ASN- 37 | 3.51 | 0 | Hydrophobic |
| C14 | CB | ASP- 40 | 3.65 | 0 | Hydrophobic |
| C3 | CB | ALA- 41 | 4.08 | 0 | Hydrophobic |
| C16 | CB | ALA- 41 | 3.99 | 0 | Hydrophobic |
| C14 | CD | LYS- 44 | 4.32 | 0 | Hydrophobic |
| C15 | CG | LYS- 44 | 4.28 | 0 | Hydrophobic |
| O6 | NZ | LYS- 44 | 2.92 | 139.65 | H-Bond (Protein Donor) |
| O3 | OD2 | ASP- 79 | 2.57 | 159.62 | H-Bond (Ligand Donor) |
| C16 | CG2 | ILE- 82 | 3.57 | 0 | Hydrophobic |
| C8 | CE | MET- 84 | 3.63 | 0 | Hydrophobic |
| C7 | CE | MET- 84 | 3.73 | 0 | Hydrophobic |
| C18 | CG | MET- 84 | 3.75 | 0 | Hydrophobic |
| C8 | CD2 | LEU- 93 | 4.41 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 93 | 4.37 | 0 | Hydrophobic |
| CL1 | CG | PHE- 124 | 3.42 | 0 | Hydrophobic |
| C3 | CB | THR- 171 | 4.22 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 173 | 3.74 | 0 | Hydrophobic |
