sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.650 Å
X-ray
2013-11-04
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 8.520 | 8.520 | 8.520 | 0.000 | 8.520 | 1 |
| 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: | 17.741 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.511 | 678.375 |
| % Hydrophobic | % Polar |
|---|---|
| 57.21 | 42.79 |
| According to VolSite | |
| HET Code: | 2LC |
|---|---|
| Formula: | C22H26FN3O3 |
| Molecular weight: | 399.459 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 69.11 % |
| Polar Surface area: | 86.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| 2.97145 | -11.1868 | -24.9098 |
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 |
| C24 | CB | ASN- 51 | 3.89 | 0 | Hydrophobic |
| C23 | CB | ASP- 54 | 4.01 | 0 | Hydrophobic |
| C21 | CB | ALA- 55 | 4.41 | 0 | Hydrophobic |
| C23 | CB | ALA- 55 | 4.07 | 0 | Hydrophobic |
| C21 | CD | LYS- 58 | 4.24 | 0 | Hydrophobic |
| C23 | CD | LYS- 58 | 4.33 | 0 | Hydrophobic |
| N26 | OD2 | ASP- 93 | 3 | 174.3 | H-Bond (Ligand Donor) |
| C21 | CG2 | ILE- 96 | 3.75 | 0 | Hydrophobic |
| C11 | SD | MET- 98 | 4.2 | 0 | Hydrophobic |
| C13 | SD | MET- 98 | 4.2 | 0 | Hydrophobic |
| C20 | CG | MET- 98 | 4.41 | 0 | Hydrophobic |
| C15 | SD | MET- 98 | 4.01 | 0 | Hydrophobic |
| C28 | CE | MET- 98 | 3.7 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 103 | 4.01 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 103 | 3.99 | 0 | Hydrophobic |
| C1 | CB | LEU- 107 | 4.29 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 107 | 3.8 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 107 | 4.27 | 0 | Hydrophobic |
| C20 | CD1 | LEU- 107 | 4.24 | 0 | Hydrophobic |
| C1 | CB | ALA- 111 | 4.04 | 0 | Hydrophobic |
| C12 | CZ | PHE- 138 | 4.25 | 0 | Hydrophobic |
| C13 | CG | PHE- 138 | 3.98 | 0 | Hydrophobic |
| C9 | CE2 | PHE- 138 | 3.87 | 0 | Hydrophobic |
| C30 | CB | PHE- 138 | 4.31 | 0 | Hydrophobic |
| O8 | OH | TYR- 139 | 2.68 | 128.74 | H-Bond (Protein Donor) |
| C9 | CZ | TYR- 139 | 4.04 | 0 | Hydrophobic |
| C12 | CG2 | VAL- 150 | 4.35 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 162 | 4.4 | 0 | Hydrophobic |
| C12 | CE2 | TRP- 162 | 3.43 | 0 | Hydrophobic |
| F29 | CG2 | THR- 184 | 3.45 | 0 | Hydrophobic |
| F29 | CG2 | VAL- 186 | 3.27 | 0 | Hydrophobic |
| O27 | O | HOH- 401 | 2.74 | 178.25 | H-Bond (Protein Donor) |
