sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.100 Å
X-ray
2010-07-28
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.100 | 7.100 | 7.100 | 0.000 | 7.100 | 2 |
| 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 | 100 % |
| B-Factor: | 10.233 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.420 | 236.250 |
| % Hydrophobic | % Polar |
|---|---|
| 42.86 | 57.14 |
| According to VolSite | |
| HET Code: | FK5 |
|---|---|
| Formula: | C44H69NO12 |
| Molecular weight: | 804.018 g/mol |
| DrugBank ID: | DB00864 |
| Buried Surface Area: | 38.98 % |
| Polar Surface area: | 178.36 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 52.564 | 15.3589 | 21.2169 |
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 | 3.8 | 0 | Hydrophobic |
| C10 | CE1 | PHE- 67 | 4.39 | 0 | Hydrophobic |
| C35 | CE1 | PHE- 67 | 4.05 | 0 | Hydrophobic |
| C10 | CB | ASP- 68 | 4.5 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 68 | 2.67 | 160.08 | H-Bond (Ligand Donor) |
| C4 | CE2 | PHE- 77 | 3.55 | 0 | Hydrophobic |
| C5 | CD2 | PHE- 77 | 3.93 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 77 | 4.13 | 0 | Hydrophobic |
| C36 | CD1 | PHE- 77 | 3.83 | 0 | Hydrophobic |
| C41 | CZ | PHE- 77 | 3.5 | 0 | Hydrophobic |
| O10 | O | GLN- 85 | 3.47 | 131.83 | H-Bond (Ligand Donor) |
| C4 | CG1 | VAL- 86 | 3.65 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 87 | 4.33 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 87 | 4.32 | 0 | Hydrophobic |
| C45 | CG2 | ILE- 87 | 4.41 | 0 | Hydrophobic |
| O2 | N | ILE- 87 | 2.9 | 147.03 | H-Bond (Protein Donor) |
| C3 | CD2 | TRP- 90 | 3.45 | 0 | Hydrophobic |
| C4 | CZ3 | TRP- 90 | 3.61 | 0 | Hydrophobic |
| C5 | CH2 | TRP- 90 | 3.78 | 0 | Hydrophobic |
| C31 | CD1 | TYR- 113 | 4.33 | 0 | Hydrophobic |
| C42 | CE1 | TYR- 113 | 3.71 | 0 | Hydrophobic |
| C45 | CD1 | TYR- 113 | 4.17 | 0 | Hydrophobic |
| C35 | CZ | TYR- 113 | 3.97 | 0 | Hydrophobic |
| C30 | CE1 | TYR- 113 | 3.77 | 0 | Hydrophobic |
| O3 | OH | TYR- 113 | 2.65 | 170.93 | H-Bond (Protein Donor) |
| C12 | CD | LYS- 121 | 4.42 | 0 | Hydrophobic |
| C35 | CG1 | ILE- 122 | 3.56 | 0 | Hydrophobic |
