sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.250 Å
X-ray
2014-12-17
| Name: | Alanine racemase, biosynthetic |
|---|---|
| ID: | ALR1_ECOLI |
| AC: | P0A6B4 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 23 % |
| B | 77 % |
| B-Factor: | 12.543 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.597 | 1039.500 |
| % Hydrophobic | % Polar |
|---|---|
| 43.51 | 56.49 |
| According to VolSite | |
| HET Code: | IN5 |
|---|---|
| Formula: | C10H15N2O8P2 |
| Molecular weight: | 353.182 g/mol |
| DrugBank ID: | DB03327 |
| Buried Surface Area: | 75.31 % |
| Polar Surface area: | 204.96 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 4 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 48.8177 | -2.02068 | -31.4581 |
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 |
| C7 | CG2 | VAL- 32 | 4.18 | 0 | Hydrophobic |
| O6 | NZ | LYS- 34 | 3.05 | 162.79 | H-Bond (Protein Donor) |
| O6 | NZ | LYS- 34 | 3.05 | 0 | Ionic (Protein Cationic) |
| C10 | CZ | TYR- 38 | 4.28 | 0 | Hydrophobic |
| O3 | OH | TYR- 38 | 2.72 | 140.47 | H-Bond (Protein Donor) |
| C3 | CD1 | LEU- 78 | 4.4 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 78 | 4.24 | 0 | Hydrophobic |
| O1 | NH2 | ARG- 129 | 3.44 | 125.69 | H-Bond (Protein Donor) |
| O7 | NH2 | ARG- 129 | 3.28 | 129.99 | H-Bond (Protein Donor) |
| O7 | NH1 | ARG- 129 | 2.74 | 158.76 | H-Bond (Protein Donor) |
| O7 | CZ | ARG- 129 | 3.41 | 0 | Ionic (Protein Cationic) |
| C6 | CB | HIS- 159 | 4.13 | 0 | Hydrophobic |
| C7 | CB | ALA- 193 | 3.64 | 0 | Hydrophobic |
| O5 | N | SER- 194 | 2.79 | 154.46 | H-Bond (Protein Donor) |
| N1 | NE | ARG- 209 | 2.81 | 157.79 | H-Bond (Protein Donor) |
| N1 | NH2 | ARG- 209 | 3.06 | 139.96 | H-Bond (Protein Donor) |
| O5 | N | GLY- 211 | 2.97 | 145.89 | H-Bond (Protein Donor) |
| O3 | N | ILE- 212 | 2.94 | 156.16 | H-Bond (Protein Donor) |
| C10 | CE | MET- 303 | 3.63 | 0 | Hydrophobic |
| O6 | N | MET- 303 | 3.34 | 136.78 | H-Bond (Protein Donor) |
| O8 | N | MET- 303 | 2.77 | 151.63 | H-Bond (Protein Donor) |
| O4 | OH | TYR- 343 | 2.67 | 164.3 | H-Bond (Protein Donor) |
| C10 | CE2 | TYR- 343 | 3.6 | 0 | Hydrophobic |
