sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 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 | 14 % |
| F | 86 % |
| B-Factor: | 5.758 |
|---|---|
| Number of residues: | 43 |
| Including | |
| Standard Amino Acids: | 42 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.188 | 324.000 |
| % Hydrophobic | % Polar |
|---|---|
| 71.88 | 28.13 |
| According to VolSite | |
| HET Code: | CAA |
|---|---|
| Formula: | C25H36N7O18P3S |
| Molecular weight: | 847.576 g/mol |
| DrugBank ID: | DB03059 |
| Buried Surface Area: | 53.22 % |
| Polar Surface area: | 446.75 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 23 |
| 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 |
|---|---|---|
| 26.9455 | -11.6269 | 103.581 |
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 |
| C1B | CB | ALA- 24 | 4.37 | 0 | Hydrophobic |
| C5B | CG | LEU- 25 | 4.07 | 0 | Hydrophobic |
| CCP | CD1 | LEU- 25 | 4.12 | 0 | Hydrophobic |
| CEP | CD1 | LEU- 25 | 4.12 | 0 | Hydrophobic |
| CEP | CB | ALA- 63 | 3.87 | 0 | Hydrophobic |
| N6A | O | ALA- 65 | 2.86 | 138.5 | H-Bond (Ligand Donor) |
| O1 | N | ALA- 65 | 3.06 | 170.52 | H-Bond (Protein Donor) |
| C2 | CB | ALA- 65 | 4.24 | 0 | Hydrophobic |
| C4 | CB | ALA- 65 | 3.57 | 0 | Hydrophobic |
| N1A | N | ILE- 67 | 2.74 | 173.93 | H-Bond (Protein Donor) |
| C6P | CD1 | ILE- 67 | 4.1 | 0 | Hydrophobic |
| C2P | CD1 | ILE- 67 | 3.84 | 0 | Hydrophobic |
| S1P | CG1 | ILE- 67 | 4.39 | 0 | Hydrophobic |
| O7A | NZ | LYS- 68 | 3.62 | 0 | Ionic (Protein Cationic) |
| S1P | CE | MET- 70 | 3.72 | 0 | Hydrophobic |
| C2 | CE | MET- 70 | 4.22 | 0 | Hydrophobic |
| C4 | CE1 | PHE- 84 | 3.8 | 0 | Hydrophobic |
| CDP | CE1 | TYR- 104 | 4.03 | 0 | Hydrophobic |
| CEP | CD2 | TYR- 104 | 3.76 | 0 | Hydrophobic |
| CCP | CZ | TYR- 104 | 3.75 | 0 | Hydrophobic |
| CDP | CD1 | LEU- 106 | 4.38 | 0 | Hydrophobic |
| CEP | CD1 | LEU- 106 | 3.8 | 0 | Hydrophobic |
| O1 | N | GLY- 108 | 2.51 | 164.33 | H-Bond (Protein Donor) |
| O3 | OE1 | GLU- 111 | 2.52 | 164.71 | H-Bond (Protein Donor) |
| S1P | CG | GLU- 131 | 4.04 | 0 | Hydrophobic |
| C2 | CG | GLU- 131 | 3.2 | 0 | Hydrophobic |
| S1P | CD1 | LEU- 134 | 3.74 | 0 | Hydrophobic |
| O3 | N | GLY- 139 | 3.11 | 160.5 | H-Bond (Protein Donor) |
| C4 | SD | MET- 140 | 3.43 | 0 | Hydrophobic |
| C2B | CZ | PHE- 246 | 4.49 | 0 | Hydrophobic |
| O7A | NZ | LYS- 249 | 3.79 | 0 | Ionic (Protein Cationic) |
| O1A | NZ | LYS- 249 | 3.61 | 0 | Ionic (Protein Cationic) |
