sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.380 Å
X-ray
2010-12-15
| Name: | Probable enoyl-CoA hydratase echA8 |
|---|---|
| ID: | ECHA8_MYCTU |
| AC: | P9WNN9 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 4.2.1.17 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| D | 13 % |
| F | 87 % |
| B-Factor: | 46.237 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.362 | 580.500 |
| % Hydrophobic | % Polar |
|---|---|
| 65.12 | 34.88 |
| According to VolSite | |
| HET Code: | BCO |
|---|---|
| Formula: | C25H38N7O17P3S |
| Molecular weight: | 833.592 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 52.25 % |
| Polar Surface area: | 429.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 22 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 22 |
| X | Y | Z |
|---|---|---|
| 23.3684 | 11.6057 | 21.2567 |
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 |
| C5 | CG | LEU- 25 | 4.11 | 0 | Hydrophobic |
| C11 | CD1 | LEU- 25 | 3.45 | 0 | Hydrophobic |
| N5 | O | ALA- 63 | 3.46 | 137.31 | H-Bond (Ligand Donor) |
| N7 | O | ALA- 63 | 3.18 | 163.57 | H-Bond (Ligand Donor) |
| C14 | CB | ALA- 63 | 4.16 | 0 | Hydrophobic |
| N5 | O | ALA- 65 | 3.3 | 143.23 | H-Bond (Ligand Donor) |
| S1 | CB | ALA- 65 | 4.46 | 0 | Hydrophobic |
| C24 | CB | ALA- 65 | 3.75 | 0 | Hydrophobic |
| O17 | N | ALA- 65 | 2.56 | 134.1 | H-Bond (Protein Donor) |
| N4 | N | ILE- 67 | 2.86 | 160.76 | H-Bond (Protein Donor) |
| C21 | CD1 | ILE- 67 | 4.1 | 0 | Hydrophobic |
| S1 | CG1 | ILE- 67 | 4.16 | 0 | Hydrophobic |
| S1 | CE | MET- 70 | 3.81 | 0 | Hydrophobic |
| C25 | SD | MET- 70 | 4.26 | 0 | Hydrophobic |
| C24 | CZ | PHE- 84 | 3.9 | 0 | Hydrophobic |
| C25 | CE2 | PHE- 84 | 3.77 | 0 | Hydrophobic |
| C11 | CE2 | TYR- 104 | 4.23 | 0 | Hydrophobic |
| C13 | CE1 | TYR- 104 | 4.4 | 0 | Hydrophobic |
| C14 | CD1 | TYR- 104 | 3.96 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 106 | 3.71 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 106 | 4.21 | 0 | Hydrophobic |
| O17 | N | GLY- 108 | 2.98 | 170.44 | H-Bond (Protein Donor) |
| S1 | CG | GLU- 131 | 4.5 | 0 | Hydrophobic |
| C25 | CG | GLU- 131 | 3.6 | 0 | Hydrophobic |
| C21 | CD1 | LEU- 134 | 3.62 | 0 | Hydrophobic |
| C25 | CE1 | PHE- 230 | 3.32 | 0 | Hydrophobic |
| O12 | MG | MG- 258 | 2.57 | 0 | Metal Acceptor |
