sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2005-02-08
| Name: | Hydroxymethylglutaryl-CoA synthase |
|---|---|
| ID: | HMGCS_ENTFL |
| AC: | Q9FD71 |
| Organism: | Enterococcus faecalis |
| Reign: | Bacteria |
| TaxID: | 1351 |
| EC Number: | 2.3.3.10 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 22.007 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.959 | 313.875 |
| % Hydrophobic | % Polar |
|---|---|
| 62.37 | 37.63 |
| According to VolSite | |
| HET Code: | COA |
|---|---|
| Formula: | C21H32N7O16P3S |
| Molecular weight: | 763.502 g/mol |
| DrugBank ID: | DB01992 |
| Buried Surface Area: | 47.54 % |
| Polar Surface area: | 426.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 21 |
| H-Bond Donors: | 6 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 3 |
| Rotatable Bonds: | 18 |
| X | Y | Z |
|---|---|---|
| 23.5772 | 49.3682 | 1.70429 |
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 |
| CCP | CD1 | ILE- 37 | 4.46 | 0 | Hydrophobic |
| OAP | O | GLY- 148 | 2.84 | 164.43 | H-Bond (Ligand Donor) |
| CEP | CG2 | THR- 152 | 3.97 | 0 | Hydrophobic |
| C6P | CG2 | VAL- 196 | 3.59 | 0 | Hydrophobic |
| C6P | CB | SER- 201 | 4.38 | 0 | Hydrophobic |
| C2P | CB | SER- 201 | 3.88 | 0 | Hydrophobic |
| C2P | CB | TYR- 205 | 4.17 | 0 | Hydrophobic |
| S1P | CD2 | TYR- 205 | 3.84 | 0 | Hydrophobic |
| S1P | CG | PRO- 235 | 3.61 | 0 | Hydrophobic |
| CEP | CE2 | TYR- 236 | 3.37 | 0 | Hydrophobic |
| C2P | SD | MET- 239 | 3.5 | 0 | Hydrophobic |
| O7A | NZ | LYS- 242 | 3.25 | 150.52 | H-Bond (Protein Donor) |
| O7A | NZ | LYS- 242 | 3.25 | 0 | Ionic (Protein Cationic) |
| O8A | NZ | LYS- 242 | 3.49 | 0 | Ionic (Protein Cationic) |
| S1P | CE2 | TYR- 306 | 4.01 | 0 | Hydrophobic |
| O5P | O | HOH- 778 | 2.67 | 151.58 | H-Bond (Protein Donor) |
