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
2011-02-11
| Name: | Transcriptional activator, LuxR/UhpA family of regulators |
|---|---|
| ID: | Q7NQP7_CHRVO |
| AC: | Q7NQP7 |
| Organism: | Chromobacterium violaceum |
| Reign: | Bacteria |
| TaxID: | 243365 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.191 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.450 | 344.250 |
| % Hydrophobic | % Polar |
|---|---|
| 75.49 | 24.51 |
| According to VolSite | |
| HET Code: | HL6 |
|---|---|
| Formula: | C10H17NO3 |
| Molecular weight: | 199.247 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 80.03 % |
| Polar Surface area: | 55.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 3 |
| H-Bond Donors: | 1 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 14.9917 | 4.9305 | 53.0351 |
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 |
| C10 | CD1 | ILE- 57 | 4.24 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 59 | 4.25 | 0 | Hydrophobic |
| C9 | CG2 | VAL- 59 | 3.85 | 0 | Hydrophobic |
| O3 | OH | TYR- 80 | 2.8 | 143.26 | H-Bond (Protein Donor) |
| C8 | CE2 | TYR- 80 | 4.15 | 0 | Hydrophobic |
| C10 | CE2 | TYR- 80 | 4.39 | 0 | Hydrophobic |
| O1 | NE1 | TRP- 84 | 2.98 | 164.86 | H-Bond (Protein Donor) |
| C10 | CD2 | LEU- 85 | 3.76 | 0 | Hydrophobic |
| C10 | CD1 | TYR- 88 | 3.98 | 0 | Hydrophobic |
| C8 | CZ | TYR- 88 | 3.9 | 0 | Hydrophobic |
| N | OD2 | ASP- 97 | 2.67 | 165.16 | H-Bond (Ligand Donor) |
| C3 | CG1 | ILE- 99 | 3.6 | 0 | Hydrophobic |
| C6 | CG2 | ILE- 99 | 4.07 | 0 | Hydrophobic |
| C6 | SD | MET- 100 | 4.14 | 0 | Hydrophobic |
| C2 | CZ3 | TRP- 111 | 3.62 | 0 | Hydrophobic |
| C3 | CE3 | TRP- 111 | 3.85 | 0 | Hydrophobic |
| C3 | CZ | PHE- 115 | 3.74 | 0 | Hydrophobic |
| C2 | CZ | PHE- 126 | 3.6 | 0 | Hydrophobic |
| C2 | CB | ALA- 130 | 3.91 | 0 | Hydrophobic |
| C2 | CB | MET- 135 | 4.36 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 153 | 3.35 | 0 | Hydrophobic |
| O3 | OG | SER- 155 | 2.81 | 152.42 | H-Bond (Protein Donor) |
