sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2008-01-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.920 | 5.920 | 5.920 | 0.000 | 5.920 | 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: | 19.735 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.942 | 509.625 |
| % Hydrophobic | % Polar |
|---|---|
| 48.34 | 51.66 |
| According to VolSite | |
| HET Code: | GDM |
|---|---|
| Formula: | C29H40N2O9 |
| Molecular weight: | 560.636 g/mol |
| DrugBank ID: | DB02424 |
| Buried Surface Area: | 57.38 % |
| Polar Surface area: | 163.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 22.8712 | -34.1469 | -4.8282 |
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 |
| C6 | CB | ASN- 37 | 4.47 | 0 | Hydrophobic |
| C25 | CB | ASN- 37 | 4 | 0 | Hydrophobic |
| C25 | CB | ASP- 40 | 4.47 | 0 | Hydrophobic |
| C26 | CB | ALA- 41 | 3.91 | 0 | Hydrophobic |
| O5 | NZ | LYS- 44 | 2.8 | 158.05 | H-Bond (Protein Donor) |
| C26 | CD | LYS- 44 | 3.64 | 0 | Hydrophobic |
| N2 | OD2 | ASP- 79 | 2.81 | 162.78 | H-Bond (Ligand Donor) |
| C26 | CG2 | ILE- 82 | 3.56 | 0 | Hydrophobic |
| C23 | SD | MET- 84 | 3.89 | 0 | Hydrophobic |
| C27 | CE | MET- 84 | 4.18 | 0 | Hydrophobic |
| C7 | SD | MET- 84 | 4.07 | 0 | Hydrophobic |
| C27 | CG | GLU- 88 | 4.3 | 0 | Hydrophobic |
| C27 | CB | ASN- 92 | 4.4 | 0 | Hydrophobic |
| C28 | CB | ASN- 92 | 4.08 | 0 | Hydrophobic |
| C22 | CD2 | LEU- 93 | 4.22 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 93 | 4.26 | 0 | Hydrophobic |
| C22 | CB | ALA- 97 | 4.39 | 0 | Hydrophobic |
| O1 | N | PHE- 124 | 2.87 | 155.98 | H-Bond (Protein Donor) |
| C22 | CB | PHE- 124 | 4.28 | 0 | Hydrophobic |
| C23 | CD1 | PHE- 124 | 3.95 | 0 | Hydrophobic |
| C22 | CE2 | TYR- 125 | 4.4 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 136 | 4.27 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 173 | 4.18 | 0 | Hydrophobic |
| O4 | O | HOH- 407 | 2.8 | 166.29 | H-Bond (Protein Donor) |
