sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2012-02-17
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 5.570 | 5.570 | 5.570 | 0.000 | 5.570 | 1 |
| Name: | Peptidyl-prolyl cis-trans isomerase FKBP5 |
|---|---|
| ID: | FKBP5_HUMAN |
| AC: | Q13451 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 5.2.1.8 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 90 % |
| B | 10 % |
| B-Factor: | 9.905 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.545 | 249.750 |
| % Hydrophobic | % Polar |
|---|---|
| 45.95 | 54.05 |
| According to VolSite | |
| HET Code: | I63 |
|---|---|
| Formula: | C32H40NO9 |
| Molecular weight: | 582.661 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 43.91 % |
| Polar Surface area: | 131.5 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 15 |
| X | Y | Z |
|---|---|---|
| 19.4201 | -14.5578 | 31.3854 |
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 |
| C5 | CZ | TYR- 57 | 3.53 | 0 | Hydrophobic |
| O4 | OH | TYR- 57 | 3.44 | 134.88 | H-Bond (Protein Donor) |
| C11 | CD1 | PHE- 67 | 3.76 | 0 | Hydrophobic |
| C13 | CB | ASP- 68 | 3.9 | 0 | Hydrophobic |
| C5 | CZ | PHE- 77 | 3.74 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 77 | 3.68 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 86 | 4.21 | 0 | Hydrophobic |
| C37 | CG2 | ILE- 87 | 3.88 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 87 | 4.36 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 87 | 3.79 | 0 | Hydrophobic |
| O2 | N | ILE- 87 | 2.92 | 159.71 | H-Bond (Protein Donor) |
| C5 | CH2 | TRP- 90 | 3.96 | 0 | Hydrophobic |
| C4 | CZ3 | TRP- 90 | 3.65 | 0 | Hydrophobic |
| C3 | CE2 | TRP- 90 | 3.37 | 0 | Hydrophobic |
| C16 | CE1 | TYR- 113 | 3.94 | 0 | Hydrophobic |
| C37 | CD1 | TYR- 113 | 3.53 | 0 | Hydrophobic |
| O3 | OH | TYR- 113 | 2.64 | 154.07 | H-Bond (Protein Donor) |
| C12 | CB | SER- 118 | 4.38 | 0 | Hydrophobic |
| C12 | CD | LYS- 121 | 4.1 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 122 | 3.79 | 0 | Hydrophobic |
| C3 | CZ | PHE- 130 | 4.28 | 0 | Hydrophobic |
| O36 | O | HOH- 307 | 3.42 | 144.98 | H-Bond (Protein Donor) |
