sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.690 Å
X-ray
2012-03-31
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.720 | 8.220 | 8.380 | 0.360 | 8.570 | 3 |
| Name: | Heat shock protein HSP 90-alpha |
|---|---|
| ID: | HS90A_HUMAN |
| AC: | P07900 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 13.156 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.485 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 40.85 | 59.15 |
| According to VolSite | |
| HET Code: | RDC |
|---|---|
| Formula: | C18H16ClO6 |
| Molecular weight: | 363.769 g/mol |
| DrugBank ID: | DB03758 |
| Buried Surface Area: | 71.53 % |
| 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 |
|---|---|---|
| 10.5109 | -5.7586 | 14.0635 |
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- 51 | 4.43 | 0 | Hydrophobic |
| C5 | CB | ASN- 51 | 3.51 | 0 | Hydrophobic |
| C14 | CB | ASP- 54 | 3.77 | 0 | Hydrophobic |
| C3 | CB | ALA- 55 | 4.18 | 0 | Hydrophobic |
| C14 | CB | ALA- 55 | 4.12 | 0 | Hydrophobic |
| C16 | CB | ALA- 55 | 3.89 | 0 | Hydrophobic |
| O6 | NZ | LYS- 58 | 3.11 | 168.67 | H-Bond (Protein Donor) |
| C16 | CD | LYS- 58 | 3.88 | 0 | Hydrophobic |
| O3 | OD2 | ASP- 93 | 2.58 | 158.26 | H-Bond (Ligand Donor) |
| O3 | OD1 | ASP- 93 | 3.44 | 127.99 | H-Bond (Ligand Donor) |
| C16 | CG2 | ILE- 96 | 3.88 | 0 | Hydrophobic |
| C8 | SD | MET- 98 | 3.67 | 0 | Hydrophobic |
| C7 | CE | MET- 98 | 4.11 | 0 | Hydrophobic |
| C18 | CG | MET- 98 | 3.69 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 107 | 4.32 | 0 | Hydrophobic |
| CL1 | CD1 | PHE- 138 | 3.4 | 0 | Hydrophobic |
| C3 | CB | THR- 184 | 3.67 | 0 | Hydrophobic |
| C2 | CG2 | THR- 184 | 4.06 | 0 | Hydrophobic |
| C4 | CG2 | THR- 184 | 3.96 | 0 | Hydrophobic |
| O2 | OG1 | THR- 184 | 2.82 | 140.11 | H-Bond (Protein Donor) |
| C5 | CG2 | VAL- 186 | 4.04 | 0 | Hydrophobic |
