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
2012-02-29
| Name: | Peptidyl-prolyl cis-trans isomerase |
|---|---|
| ID: | Q3JK38_BURP1 |
| AC: | Q3JK38 |
| Organism: | Burkholderia pseudomallei |
| Reign: | Bacteria |
| TaxID: | 320372 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 22 % |
| B | 78 % |
| B-Factor: | 20.938 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.389 | 236.250 |
| % Hydrophobic | % Polar |
|---|---|
| 52.86 | 47.14 |
| According to VolSite | |
| HET Code: | FK5 |
|---|---|
| Formula: | C44H69NO12 |
| Molecular weight: | 804.018 g/mol |
| DrugBank ID: | DB00864 |
| Buried Surface Area: | 44.06 % |
| 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 |
|---|---|---|
| 35.7659 | 14.6456 | 12.8253 |
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- 33 | 3.71 | 0 | Hydrophobic |
| C35 | CE1 | PHE- 43 | 4.36 | 0 | Hydrophobic |
| C10 | CB | ASP- 44 | 4.41 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 44 | 2.7 | 156.21 | H-Bond (Ligand Donor) |
| C44 | CD | ARG- 49 | 4.49 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 53 | 3.95 | 0 | Hydrophobic |
| C36 | CD1 | PHE- 53 | 3.66 | 0 | Hydrophobic |
| C41 | CZ | PHE- 53 | 3.69 | 0 | Hydrophobic |
| C4 | CE2 | PHE- 53 | 3.57 | 0 | Hydrophobic |
| C37 | SD | MET- 61 | 3.95 | 0 | Hydrophobic |
| C23 | CE | MET- 61 | 3.73 | 0 | Hydrophobic |
| O10 | O | MET- 61 | 2.72 | 140.53 | H-Bond (Ligand Donor) |
| C3 | CB | VAL- 62 | 4.41 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 62 | 3.94 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 63 | 4.14 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 63 | 3.99 | 0 | Hydrophobic |
| C45 | CG2 | ILE- 63 | 4.48 | 0 | Hydrophobic |
| O2 | N | ILE- 63 | 2.82 | 154.01 | H-Bond (Protein Donor) |
| C3 | CE2 | TRP- 66 | 3.46 | 0 | Hydrophobic |
| C4 | CD2 | TRP- 66 | 3.67 | 0 | Hydrophobic |
| C5 | CZ2 | TRP- 66 | 3.9 | 0 | Hydrophobic |
| C35 | CZ | TYR- 89 | 4.12 | 0 | Hydrophobic |
| C42 | CE1 | TYR- 89 | 4.1 | 0 | Hydrophobic |
| C45 | CD1 | TYR- 89 | 3.91 | 0 | Hydrophobic |
| C30 | CE1 | TYR- 89 | 3.86 | 0 | Hydrophobic |
| O3 | OH | TYR- 89 | 2.63 | 175.69 | H-Bond (Protein Donor) |
| C35 | CD1 | ILE- 98 | 3.75 | 0 | Hydrophobic |
