sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2009-03-16
| Name: | Glutaryl-CoA dehydrogenase |
|---|---|
| ID: | Q3JP94_BURP1 |
| AC: | Q3JP94 |
| Organism: | Burkholderia pseudomallei |
| Reign: | Bacteria |
| TaxID: | 320372 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 100 % |
| B-Factor: | 34.691 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.488 | 739.125 |
| % Hydrophobic | % Polar |
|---|---|
| 63.93 | 36.07 |
| According to VolSite | |
| HET Code: | QQQ |
|---|---|
| Formula: | C10H11N2O3S |
| Molecular weight: | 239.271 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.33 % |
| Polar Surface area: | 83.4 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| -32.0589 | 47.9978 | 35.6703 |
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 |
| O12 | NH2 | ARG- 97 | 2.81 | 139.83 | H-Bond (Protein Donor) |
| O12 | NH1 | ARG- 97 | 2.73 | 144.36 | H-Bond (Protein Donor) |
| O12 | CZ | ARG- 97 | 3.18 | 0 | Ionic (Protein Cationic) |
| C14 | CB | SER- 98 | 4.42 | 0 | Hydrophobic |
| C16 | CB | SER- 101 | 3.43 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 102 | 4.4 | 0 | Hydrophobic |
| C16 | CG2 | VAL- 102 | 4.12 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 106 | 4.19 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 106 | 4.48 | 0 | Hydrophobic |
| C15 | CB | THR- 171 | 4.43 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 250 | 3.82 | 0 | Hydrophobic |
| C6 | CB | ALA- 253 | 3.71 | 0 | Hydrophobic |
| C5 | CG | ARG- 254 | 4.32 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 257 | 3.77 | 0 | Hydrophobic |
| C2 | CD1 | ILE- 257 | 3.83 | 0 | Hydrophobic |
| C15 | CZ | TYR- 373 | 3.75 | 0 | Hydrophobic |
| C4 | CG | GLU- 374 | 3.7 | 0 | Hydrophobic |
