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
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 |
|---|---|
| D | 100 % |
| B-Factor: | 34.659 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.177 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 74.19 | 25.81 |
| According to VolSite | |
| HET Code: | HL0 |
|---|---|
| Formula: | C14H25NO3 |
| Molecular weight: | 255.353 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 75.76 % |
| 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: | 9 |
| X | Y | Z |
|---|---|---|
| 30.3439 | 33.5001 | 17.3649 |
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 |
| C3 | CD1 | ILE- 57 | 4.06 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 57 | 4.26 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 59 | 3.98 | 0 | Hydrophobic |
| C7 | CG2 | VAL- 59 | 4.01 | 0 | Hydrophobic |
| C5 | CE | MET- 72 | 4.11 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 75 | 4.38 | 0 | Hydrophobic |
| C3 | CG1 | VAL- 75 | 4.32 | 0 | Hydrophobic |
| O1 | OH | TYR- 80 | 2.63 | 145.17 | H-Bond (Protein Donor) |
| C6 | CE1 | TYR- 80 | 4.48 | 0 | Hydrophobic |
| O3 | NE1 | TRP- 84 | 2.92 | 168.72 | H-Bond (Protein Donor) |
| C3 | CD2 | LEU- 85 | 3.97 | 0 | Hydrophobic |
| C4 | CE2 | TYR- 88 | 3.76 | 0 | Hydrophobic |
| C6 | CZ | TYR- 88 | 4.01 | 0 | Hydrophobic |
| C2 | CD2 | TYR- 88 | 3.86 | 0 | Hydrophobic |
| N | OD2 | ASP- 97 | 2.83 | 161.54 | H-Bond (Ligand Donor) |
| C12 | CG1 | ILE- 99 | 3.83 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 99 | 3.73 | 0 | Hydrophobic |
| C8 | SD | MET- 100 | 3.66 | 0 | Hydrophobic |
| C12 | CE3 | TRP- 111 | 3.85 | 0 | Hydrophobic |
| C13 | CZ3 | TRP- 111 | 3.75 | 0 | Hydrophobic |
| C12 | CZ | PHE- 115 | 3.69 | 0 | Hydrophobic |
| C13 | CZ | PHE- 126 | 3.71 | 0 | Hydrophobic |
| C13 | CB | ALA- 130 | 3.7 | 0 | Hydrophobic |
| C13 | CB | MET- 135 | 4.19 | 0 | Hydrophobic |
| C9 | CD1 | ILE- 153 | 4.45 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 153 | 3.53 | 0 | Hydrophobic |
| O1 | OG | SER- 155 | 2.88 | 156.59 | H-Bond (Protein Donor) |
| C8 | CB | SER- 155 | 4.5 | 0 | Hydrophobic |
