sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2007-09-24
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.050 | 8.380 | 8.380 | 0.320 | 8.700 | 2 |
| 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: | 33.049 |
|---|---|
| Number of residues: | 39 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.285 | 465.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.75 | 57.25 |
| According to VolSite | |
| HET Code: | 2GJ |
|---|---|
| Formula: | C26H32N3O5 |
| Molecular weight: | 466.549 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.39 % |
| Polar Surface area: | 109.26 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 32.5012 | 8.33435 | 24.9339 |
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 |
| O34 | ND2 | ASN- 51 | 3.34 | 162.86 | H-Bond (Protein Donor) |
| C21 | CB | ASN- 51 | 3.83 | 0 | Hydrophobic |
| C15 | CB | ASN- 51 | 3.34 | 0 | Hydrophobic |
| C21 | CB | ASP- 54 | 4.37 | 0 | Hydrophobic |
| C22 | CB | ALA- 55 | 4.2 | 0 | Hydrophobic |
| C17 | CB | ALA- 55 | 4.08 | 0 | Hydrophobic |
| O9 | NZ | LYS- 58 | 3.28 | 125.19 | H-Bond (Protein Donor) |
| C12 | CD | LYS- 58 | 4.46 | 0 | Hydrophobic |
| N10 | O | GLY- 97 | 2.78 | 159.72 | H-Bond (Ligand Donor) |
| C18 | SD | MET- 98 | 4.05 | 0 | Hydrophobic |
| C32 | CE | MET- 98 | 3.93 | 0 | Hydrophobic |
| C13 | CE | MET- 98 | 3.55 | 0 | Hydrophobic |
| C32 | CG | LEU- 107 | 4.01 | 0 | Hydrophobic |
| C31 | CB | LEU- 107 | 3.89 | 0 | Hydrophobic |
| C31 | CG2 | THR- 109 | 4.38 | 0 | Hydrophobic |
| C19 | CG2 | THR- 109 | 3.73 | 0 | Hydrophobic |
| C31 | CB | PHE- 138 | 3.93 | 0 | Hydrophobic |
| C32 | CD1 | PHE- 138 | 3.43 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 150 | 4.38 | 0 | Hydrophobic |
| O5 | OG1 | THR- 184 | 2.9 | 131.99 | H-Bond (Protein Donor) |
| C17 | CB | THR- 184 | 3.83 | 0 | Hydrophobic |
| C6 | CG2 | THR- 184 | 4.1 | 0 | Hydrophobic |
| C16 | CG2 | THR- 184 | 4.08 | 0 | Hydrophobic |
| C32 | CG2 | VAL- 186 | 4.36 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 186 | 4.12 | 0 | Hydrophobic |
