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
1998-08-06
| Name: | Aromatic-amino-acid aminotransferase |
|---|---|
| ID: | TYRB_PARDE |
| AC: | P95468 |
| Organism: | Paracoccus denitrificans |
| Reign: | Bacteria |
| TaxID: | 266 |
| EC Number: | 2.6.1.57 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 22 % |
| B | 78 % |
| B-Factor: | 25.137 |
|---|---|
| Number of residues: | 25 |
| Including | |
| Standard Amino Acids: | 22 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.694 | 513.000 |
| % Hydrophobic | % Polar |
|---|---|
| 50.00 | 50.00 |
| According to VolSite | |
| HET Code: | CXP |
|---|---|
| Formula: | C9H15O2 |
| Molecular weight: | 155.214 g/mol |
| DrugBank ID: | DB02242 |
| Buried Surface Area: | 79.77 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| 101.104 | 45.3148 | 12.1927 |
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 |
| C2 | CD1 | ILE- 17 | 4.44 | 0 | Hydrophobic |
| C4 | CD1 | LEU- 18 | 4.28 | 0 | Hydrophobic |
| C7 | CG1 | VAL- 37 | 4.38 | 0 | Hydrophobic |
| O1 | N | GLY- 38 | 2.78 | 149.92 | H-Bond (Protein Donor) |
| C6 | CZ | TYR- 70 | 3.68 | 0 | Hydrophobic |
| C7 | CE2 | TYR- 70 | 3.64 | 0 | Hydrophobic |
| O2 | NE1 | TRP- 140 | 2.83 | 132.04 | H-Bond (Protein Donor) |
| C1 | CZ2 | TRP- 140 | 3.72 | 0 | Hydrophobic |
| O2 | ND2 | ASN- 194 | 2.89 | 158.36 | H-Bond (Protein Donor) |
| C5 | CB | SER- 296 | 4.21 | 0 | Hydrophobic |
| C5 | CE1 | PHE- 297 | 3.98 | 0 | Hydrophobic |
| O1 | CZ | ARG- 386 | 3.78 | 0 | Ionic (Protein Cationic) |
| O1 | NH1 | ARG- 386 | 3.4 | 141.55 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 386 | 3.26 | 147.59 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 386 | 3.1 | 148.23 | H-Bond (Protein Donor) |
