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
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 | 73 % |
| B | 27 % |
| B-Factor: | 18.048 |
|---|---|
| Number of residues: | 23 |
| Including | |
| Standard Amino Acids: | 21 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.187 | 1147.500 |
| % Hydrophobic | % Polar |
|---|---|
| 50.59 | 49.41 |
| According to VolSite | |
| HET Code: | 5PV |
|---|---|
| Formula: | C11H13O2 |
| Molecular weight: | 177.220 g/mol |
| DrugBank ID: | DB04051 |
| Buried Surface Area: | 68.58 % |
| Polar Surface area: | 40.12 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 2 |
| H-Bond Donors: | 0 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 93.6743 | 17.607 | -2.08508 |
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 |
| C6 | CD1 | ILE- 17 | 4.18 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 17 | 4.27 | 0 | Hydrophobic |
| C7 | CE2 | TYR- 70 | 3.31 | 0 | Hydrophobic |
| C9 | CZ2 | TRP- 140 | 4.06 | 0 | Hydrophobic |
| C3 | CZ2 | TRP- 140 | 3.27 | 0 | Hydrophobic |
| O1 | NE1 | TRP- 140 | 2.8 | 129.98 | H-Bond (Protein Donor) |
| O1 | ND2 | ASN- 194 | 3 | 154.99 | H-Bond (Protein Donor) |
| C4 | CB | SER- 296 | 3.37 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 297 | 4.27 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 386 | 3.28 | 143.79 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 386 | 2.9 | 142.14 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 386 | 3.16 | 132.26 | H-Bond (Protein Donor) |
| O2 | CZ | ARG- 386 | 3.44 | 0 | Ionic (Protein Cationic) |
