sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2008-09-30
| Name: | DNA-directed RNA polymerase subunit beta | DNA-directed RNA polymerase subunit beta' |
|---|---|---|
| ID: | RPOB_THET8 | RPOC_THET8 |
| AC: | Q8RQE9 | Q8RQE8 |
| Organism: | Thermus thermophilus | |
| Reign: | Bacteria | |
| TaxID: | 300852 | |
| EC Number: | / | |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| C | 39 % |
| D | 61 % |
| B-Factor: | 39.591 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.549 | 769.500 |
| % Hydrophobic | % Polar |
|---|---|
| 59.21 | 40.79 |
| According to VolSite | |
| HET Code: | MXP |
|---|---|
| Formula: | C23H30NO6 |
| Molecular weight: | 416.487 g/mol |
| DrugBank ID: | DB08226 |
| Buried Surface Area: | 62.64 % |
| Polar Surface area: | 104.76 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 12 |
| X | Y | Z |
|---|---|---|
| -10.17 | 58.3987 | 5.69247 |
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 |
| C14 | CD1 | LEU- 607 | 4.26 | 0 | Hydrophobic |
| C15 | CB | LYS- 610 | 3.28 | 0 | Hydrophobic |
| C11 | CB | GLN- 611 | 3.41 | 0 | Hydrophobic |
| C16 | CG | GLN- 611 | 3.91 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 619 | 3.75 | 0 | Hydrophobic |
| O1 | N | GLY- 620 | 3.36 | 131.2 | H-Bond (Protein Donor) |
| C19 | CG | GLU- 1034 | 4.31 | 0 | Hydrophobic |
| O6 | OE1 | GLU- 1034 | 3.16 | 162.91 | H-Bond (Protein Donor) |
| C19 | CG2 | VAL- 1037 | 4.02 | 0 | Hydrophobic |
| O6 | NE1 | TRP- 1038 | 3.47 | 175.85 | H-Bond (Protein Donor) |
| O2 | OG | SER- 1084 | 3.43 | 139.52 | H-Bond (Protein Donor) |
| C14 | CD1 | LEU- 1088 | 3.72 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 1088 | 4.29 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 1088 | 3.66 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 1092 | 4.36 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 1099 | 4.1 | 0 | Hydrophobic |
| C23 | CB | HIS- 1103 | 3.76 | 0 | Hydrophobic |
| C14 | CB | ALA- 1438 | 3.82 | 0 | Hydrophobic |
| C12 | CB | ALA- 1438 | 4 | 0 | Hydrophobic |
| C23 | CB | LYS- 1463 | 3.5 | 0 | Hydrophobic |
| O6 | NZ | LYS- 1463 | 2.98 | 140.11 | H-Bond (Protein Donor) |
| C18 | CG1 | VAL- 1466 | 4.4 | 0 | Hydrophobic |
| C16 | CG1 | ILE- 1467 | 3.32 | 0 | Hydrophobic |
