sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.500 Å
X-ray
2007-01-10
| Name: | Glutamate racemase |
|---|---|
| ID: | MURI_STRP1 |
| AC: | Q9A1B7 |
| Organism: | Streptococcus pyogenes serotype M1 |
| Reign: | Bacteria |
| TaxID: | 301447 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 50.872 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.220 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 46.67 | 53.33 |
| According to VolSite | |
| HET Code: | NHL |
|---|---|
| Formula: | C16H16NO4 |
| Molecular weight: | 286.303 g/mol |
| DrugBank ID: | DB08272 |
| Buried Surface Area: | 56.23 % |
| Polar Surface area: | 107.9 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| H-Bond Donors: | 1 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 36.3189 | 34.6287 | 69.9896 |
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 |
| N | OG | SER- 11 | 2.82 | 160.7 | H-Bond (Ligand Donor) |
| CB | CB | SER- 11 | 4.07 | 0 | Hydrophobic |
| C10 | CB | SER- 11 | 3.39 | 0 | Hydrophobic |
| C6 | CB | ASP- 36 | 3.57 | 0 | Hydrophobic |
| C8 | CD1 | ILE- 50 | 4.09 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 50 | 4.06 | 0 | Hydrophobic |
| C1 | CB | TYR- 53 | 3.47 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 57 | 3.7 | 0 | Hydrophobic |
| C7 | SG | CYS- 73 | 4.05 | 0 | Hydrophobic |
| C8 | CG2 | THR- 75 | 3.46 | 0 | Hydrophobic |
| C7 | CB | ALA- 76 | 4.25 | 0 | Hydrophobic |
| C2 | CB | ALA- 76 | 4.3 | 0 | Hydrophobic |
| C11 | SD | MET- 119 | 3.86 | 0 | Hydrophobic |
