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 | 77 % |
| B | 23 % |
| B-Factor: | 16.493 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 25 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.198 | 1360.125 |
| % Hydrophobic | % Polar |
|---|---|
| 50.87 | 49.13 |
| According to VolSite | |
| HET Code: | MPP |
|---|---|
| Formula: | C11H13O4 |
| Molecular weight: | 209.219 g/mol |
| DrugBank ID: | DB04208 |
| Buried Surface Area: | 68.51 % |
| Polar Surface area: | 58.59 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 4 |
| 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 |
|---|---|---|
| 94.149 | 17.6955 | -2.04767 |
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 |
| CE2 | CD1 | ILE- 17 | 3.87 | 0 | Hydrophobic |
| CB | CE2 | TYR- 70 | 3.7 | 0 | Hydrophobic |
| CEA | CZ | TYR- 70 | 3.69 | 0 | Hydrophobic |
| OT1 | NE1 | TRP- 140 | 3 | 131.61 | H-Bond (Protein Donor) |
| CEA | CZ2 | TRP- 140 | 4.06 | 0 | Hydrophobic |
| OZA | ND2 | ASN- 142 | 2.99 | 155.92 | H-Bond (Protein Donor) |
| OT1 | ND2 | ASN- 194 | 2.89 | 164.61 | H-Bond (Protein Donor) |
| OEA | OG | SER- 296 | 2.86 | 178.15 | H-Bond (Protein Donor) |
| CEA | CB | SER- 296 | 4.08 | 0 | Hydrophobic |
| CEA | CE2 | PHE- 297 | 4.28 | 0 | Hydrophobic |
| CZA | CE2 | PHE- 297 | 3.92 | 0 | Hydrophobic |
| OT1 | NH1 | ARG- 386 | 2.87 | 151.12 | H-Bond (Protein Donor) |
| OT2 | NH1 | ARG- 386 | 3.32 | 149.58 | H-Bond (Protein Donor) |
| OT2 | NH2 | ARG- 386 | 3.26 | 153.35 | H-Bond (Protein Donor) |
| OT1 | CZ | ARG- 386 | 3.96 | 0 | Ionic (Protein Cationic) |
| OT2 | CZ | ARG- 386 | 3.75 | 0 | Ionic (Protein Cationic) |
