sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.600 Å
X-ray
2004-04-07
| Name: | 3-hydroxy-3-methylglutaryl-coenzyme A reductase |
|---|---|
| ID: | MVAA_PSEMV |
| AC: | P13702 |
| Organism: | Pseudomonas mevalonii |
| Reign: | Bacteria |
| TaxID: | 32044 |
| EC Number: | 1.1.1.88 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 69 % |
| B | 31 % |
| B-Factor: | 15.504 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.475 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 47.80 | 52.20 |
| According to VolSite | |
| HET Code: | LVA |
|---|---|
| Formula: | C24H37O6 |
| Molecular weight: | 421.547 g/mol |
| DrugBank ID: | DB03785 |
| Buried Surface Area: | 49.9 % |
| Polar Surface area: | 106.89 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 82.21 | 126.936 | 107.341 |
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 |
| O8 | OE2 | GLU- 83 | 3.32 | 153.74 | H-Bond (Ligand Donor) |
| C20 | CB | SER- 85 | 4.37 | 0 | Hydrophobic |
| C19 | CB | SER- 85 | 3.72 | 0 | Hydrophobic |
| C20 | CG1 | ILE- 86 | 4.02 | 0 | Hydrophobic |
| C20 | CB | ALA- 89 | 4.47 | 0 | Hydrophobic |
| C25 | CD1 | ILE- 213 | 3.9 | 0 | Hydrophobic |
| O3 | CZ | ARG- 261 | 3.7 | 0 | Ionic (Protein Cationic) |
| O3 | NH2 | ARG- 261 | 2.65 | 154.36 | H-Bond (Protein Donor) |
| C21 | CG2 | THR- 264 | 3.27 | 0 | Hydrophobic |
| O8 | NZ | LYS- 267 | 2.83 | 169.9 | H-Bond (Protein Donor) |
| O8 | ND2 | ASN- 271 | 3.07 | 137.72 | H-Bond (Protein Donor) |
| C11 | CB | ALA- 368 | 4.12 | 0 | Hydrophobic |
| C23 | CB | ALA- 371 | 4.42 | 0 | Hydrophobic |
| C28 | CB | ALA- 371 | 4.26 | 0 | Hydrophobic |
| C28 | CD2 | LEU- 372 | 4.22 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 372 | 3.85 | 0 | Hydrophobic |
| O1 | O | HOH- 1001 | 2.52 | 138.67 | H-Bond (Protein Donor) |
