sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.620 Å
X-ray
2015-07-24
| 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 |
|---|---|
| D | 100 % |
| B-Factor: | 19.682 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 1.390 | 1130.625 |
| % Hydrophobic | % Polar |
|---|---|
| 60.30 | 39.70 |
| According to VolSite | |
| HET Code: | NTD |
|---|---|
| Formula: | C14H9F3NO5 |
| Molecular weight: | 328.220 g/mol |
| DrugBank ID: | DB08307 |
| Buried Surface Area: | 64.23 % |
| Polar Surface area: | 103.02 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 0 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -3.56983 | 6.33517 | 43.7523 |
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 | CG2 | VAL- 228 | 4.33 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 265 | 4.01 | 0 | Hydrophobic |
| C2 | CB | PRO- 280 | 4.27 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 368 | 4.29 | 0 | Hydrophobic |
| C8 | CZ | PHE- 381 | 3.29 | 0 | Hydrophobic |
| F1 | CE1 | PHE- 381 | 3.61 | 0 | Hydrophobic |
| C6 | CB | PHE- 419 | 4.2 | 0 | Hydrophobic |
| C12 | CB | ASN- 423 | 4.49 | 0 | Hydrophobic |
| F3 | CB | ASN- 423 | 3.48 | 0 | Hydrophobic |
| C14 | CE1 | PHE- 424 | 4.21 | 0 | Hydrophobic |
| F2 | CZ | PHE- 424 | 4.09 | 0 | Hydrophobic |
| F3 | CD1 | PHE- 424 | 3.74 | 0 | Hydrophobic |
| F3 | CD2 | LEU- 427 | 4.21 | 0 | Hydrophobic |
| F1 | CD2 | LEU- 427 | 4.09 | 0 | Hydrophobic |
| O1 | FE | FE- 501 | 2.53 | 0 | Metal Acceptor |
| O7 | FE | FE- 501 | 1.99 | 0 | Metal Acceptor |
