sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.210 Å
X-ray
2007-02-07
| Name: | Putative glutaryl-CoA dehydrogenase |
|---|---|
| ID: | Q5SK63_THET8 |
| AC: | Q5SK63 |
| Organism: | Thermus thermophilus |
| Reign: | Bacteria |
| TaxID: | 300852 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 34 % |
| D | 64 % |
| E | 2 % |
| B-Factor: | 20.829 |
|---|---|
| Number of residues: | 60 |
| Including | |
| Standard Amino Acids: | 59 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.461 | 1947.375 |
| % Hydrophobic | % Polar |
|---|---|
| 52.69 | 47.31 |
| According to VolSite | |
| HET Code: | FAD |
|---|---|
| Formula: | C27H31N9O15P2 |
| Molecular weight: | 783.534 g/mol |
| DrugBank ID: | DB03147 |
| Buried Surface Area: | 69.85 % |
| Polar Surface area: | 381.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 7 |
| Rings: | 6 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 42.0409 | -3.45626 | -27.9357 |
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 |
| N3 | O | PHE- 129 | 2.98 | 135.79 | H-Bond (Ligand Donor) |
| O2 | N | LEU- 131 | 3.24 | 140.87 | H-Bond (Protein Donor) |
| N1 | OG1 | THR- 132 | 2.78 | 163.27 | H-Bond (Protein Donor) |
| O2 | N | THR- 132 | 2.99 | 167.65 | H-Bond (Protein Donor) |
| C1' | CB | THR- 132 | 3.63 | 0 | Hydrophobic |
| C3' | CG2 | THR- 132 | 4.09 | 0 | Hydrophobic |
| O5' | N | GLY- 137 | 3.48 | 120.96 | H-Bond (Protein Donor) |
| O2P | N | GLY- 137 | 2.58 | 148.28 | H-Bond (Protein Donor) |
| O2A | N | SER- 138 | 3.05 | 146.64 | H-Bond (Protein Donor) |
| O2A | OG | SER- 138 | 2.89 | 154.27 | H-Bond (Protein Donor) |
| C1' | CB | TRP- 163 | 3.89 | 0 | Hydrophobic |
| C9 | CB | TRP- 163 | 3.33 | 0 | Hydrophobic |
| O4 | N | THR- 165 | 3.03 | 156.93 | H-Bond (Protein Donor) |
| N5 | OG1 | THR- 165 | 3.21 | 157.5 | H-Bond (Protein Donor) |
| C7M | CD2 | LEU- 207 | 3.69 | 0 | Hydrophobic |
| C6 | CG2 | THR- 212 | 4.25 | 0 | Hydrophobic |
| O1A | CZ | ARG- 270 | 3.53 | 0 | Ionic (Protein Cationic) |
| O2P | NH1 | ARG- 270 | 3.48 | 167.55 | H-Bond (Protein Donor) |
| C5B | CD2 | LEU- 277 | 3.94 | 0 | Hydrophobic |
| C4B | CD1 | LEU- 277 | 4.15 | 0 | Hydrophobic |
| C1B | CD1 | LEU- 277 | 3.66 | 0 | Hydrophobic |
| N1A | NE2 | GLN- 281 | 3.19 | 123.62 | H-Bond (Protein Donor) |
| O3B | O | ASP- 338 | 3.14 | 146.91 | H-Bond (Ligand Donor) |
| O1P | N | GLY- 342 | 3.15 | 154.36 | H-Bond (Protein Donor) |
| C7M | CD1 | ILE- 345 | 3.98 | 0 | Hydrophobic |
| C8M | CD1 | ILE- 345 | 3.87 | 0 | Hydrophobic |
| C8M | CG2 | THR- 360 | 4.19 | 0 | Hydrophobic |
| C7M | CG2 | THR- 360 | 3.36 | 0 | Hydrophobic |
| C5' | CG2 | THR- 363 | 3.69 | 0 | Hydrophobic |
| C9A | CB | TYR- 364 | 3.87 | 0 | Hydrophobic |
| C2' | CB | TYR- 364 | 3.54 | 0 | Hydrophobic |
| O2B | OG1 | THR- 367 | 2.88 | 159.86 | H-Bond (Protein Donor) |
| C5' | CG2 | THR- 367 | 4.03 | 0 | Hydrophobic |
| C2B | CG2 | THR- 367 | 4.04 | 0 | Hydrophobic |
| N6A | O | PHE- 385 | 2.81 | 149.37 | H-Bond (Ligand Donor) |
| O1P | O | HOH- 1048 | 2.79 | 179.95 | H-Bond (Protein Donor) |
