sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.600 Å
X-ray
2014-01-10
| Name: | Peptidyl-prolyl cis-trans isomerase |
|---|---|
| ID: | Q5SLE7_THET8 |
| AC: | Q5SLE7 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 60 % |
| C | 40 % |
| B-Factor: | 20.319 |
|---|---|
| Number of residues: | 46 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | CL MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.287 | 688.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.98 | 49.02 |
| According to VolSite | |
| HET Code: | FK5 |
|---|---|
| Formula: | C44H69NO12 |
| Molecular weight: | 804.018 g/mol |
| DrugBank ID: | DB00864 |
| Buried Surface Area: | 49.98 % |
| 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 |
|---|---|---|
| 43.906 | 28.4591 | 12.3364 |
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 |
| C4 | CD1 | ILE- 11 | 4.37 | 0 | Hydrophobic |
| C5 | CZ | TYR- 13 | 4.02 | 0 | Hydrophobic |
| C36 | CZ | TYR- 13 | 4.21 | 0 | Hydrophobic |
| C35 | CD2 | LEU- 15 | 4.31 | 0 | Hydrophobic |
| O6 | OD2 | ASP- 23 | 2.82 | 160.18 | H-Bond (Ligand Donor) |
| C37 | CD1 | LEU- 27 | 4.48 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 27 | 3.71 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 27 | 3.75 | 0 | Hydrophobic |
| O10 | O | ASN- 35 | 2.58 | 148.94 | H-Bond (Ligand Donor) |
| C26 | CD2 | LEU- 36 | 4.2 | 0 | Hydrophobic |
| C41 | CD2 | LEU- 36 | 3.97 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 36 | 4 | 0 | Hydrophobic |
| C3 | CG1 | ILE- 37 | 4.1 | 0 | Hydrophobic |
| C30 | CG2 | ILE- 37 | 3.78 | 0 | Hydrophobic |
| C45 | CG2 | ILE- 37 | 4.46 | 0 | Hydrophobic |
| O2 | N | ILE- 37 | 2.86 | 156.94 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 40 | 3.46 | 0 | Hydrophobic |
| C30 | CE2 | TYR- 63 | 4.3 | 0 | Hydrophobic |
| C42 | CZ | TYR- 63 | 4.47 | 0 | Hydrophobic |
| C45 | CD2 | TYR- 63 | 3.65 | 0 | Hydrophobic |
| C35 | CZ | TYR- 63 | 3.82 | 0 | Hydrophobic |
| O3 | OH | TYR- 63 | 2.79 | 175.4 | H-Bond (Protein Donor) |
| C18 | CB | ALA- 78 | 3.58 | 0 | Hydrophobic |
| C37 | CB | ALA- 78 | 4.35 | 0 | Hydrophobic |
| C38 | CB | ALA- 93 | 4.33 | 0 | Hydrophobic |
| C33 | CB | GLN- 94 | 4.07 | 0 | Hydrophobic |
| O12 | O | ASP- 95 | 2.87 | 167.18 | H-Bond (Ligand Donor) |
| C35 | CD1 | LEU- 121 | 3.6 | 0 | Hydrophobic |
| C3 | CZ | PHE- 128 | 4.19 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 128 | 4.41 | 0 | Hydrophobic |
