sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.800 Å
X-ray
2004-05-27
| Name: | 4-hydroxyphenylpyruvate dioxygenase |
|---|---|
| ID: | HPPD_ARATH |
| AC: | P93836 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 1.13.11.27 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 18.721 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 1.240 | 651.375 |
| % Hydrophobic | % Polar |
|---|---|
| 66.32 | 33.68 |
| According to VolSite | |
| HET Code: | 869 |
|---|---|
| Formula: | C23H25N2O5S |
| Molecular weight: | 441.520 g/mol |
| DrugBank ID: | DB02850 |
| Buried Surface Area: | 61.72 % |
| Polar Surface area: | 109.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 0 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 43.9623 | 38.2996 | 53.0828 |
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 |
| C21 | CG1 | VAL- 207 | 3.95 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 207 | 4.41 | 0 | Hydrophobic |
| C21 | CB | SER- 246 | 4.14 | 0 | Hydrophobic |
| C23 | CB | SER- 246 | 3.77 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 248 | 3.85 | 0 | Hydrophobic |
| C23 | CG2 | VAL- 248 | 3.97 | 0 | Hydrophobic |
| C22 | CB | PRO- 259 | 3.41 | 0 | Hydrophobic |
| C31 | CE | MET- 314 | 4.32 | 0 | Hydrophobic |
| C24 | SD | MET- 314 | 3.39 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 360 | 3.66 | 0 | Hydrophobic |
| C1 | CZ | PHE- 360 | 3.33 | 0 | Hydrophobic |
| C25 | CB | PHE- 360 | 4.21 | 0 | Hydrophobic |
| C7 | CZ | PHE- 371 | 4.04 | 0 | Hydrophobic |
| C20 | CB | PHE- 398 | 4.15 | 0 | Hydrophobic |
| C22 | CG | PHE- 398 | 3.54 | 0 | Hydrophobic |
| C4 | CB | ASN- 402 | 4.26 | 0 | Hydrophobic |
| C14 | CD2 | PHE- 403 | 3.61 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 406 | 4.2 | 0 | Hydrophobic |
| O19 | FE | FE- 425 | 2.25 | 0 | Metal Acceptor |
| O10 | FE | FE- 425 | 2.41 | 0 | Metal Acceptor |
