sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.100 Å
X-ray
2010-03-18
| Name: | Pteridine reductase |
|---|---|
| ID: | O76290_TRYBB |
| AC: | O76290 |
| Organism: | Trypanosoma brucei brucei |
| Reign: | Eukaryota |
| TaxID: | 5702 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 97 % |
| D | 3 % |
| B-Factor: | 12.020 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.399 | 654.750 |
| % Hydrophobic | % Polar |
|---|---|
| 46.91 | 53.09 |
| According to VolSite | |
| HET Code: | LYA |
|---|---|
| Formula: | C20H19N5O6 |
| Molecular weight: | 425.395 g/mol |
| DrugBank ID: | DB00642 |
| Buried Surface Area: | 56.63 % |
| Polar Surface area: | 192.63 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 7.61477 | -14.5495 | 17.2536 |
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 |
| N19 | OG | SER- 95 | 2.93 | 158.13 | H-Bond (Ligand Donor) |
| C8 | CZ | PHE- 97 | 4.35 | 0 | Hydrophobic |
| DuAr | DuAr | PHE- 97 | 3.81 | 0 | Aromatic Face/Face |
| C5 | SG | CYS- 168 | 3.77 | 0 | Hydrophobic |
| N11 | OH | TYR- 174 | 3.01 | 154.21 | H-Bond (Ligand Donor) |
| C7 | CG1 | VAL- 206 | 4.33 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 209 | 4.09 | 0 | Hydrophobic |
| C8 | CG | PRO- 210 | 4.27 | 0 | Hydrophobic |
| C2 | CG | PRO- 210 | 3.58 | 0 | Hydrophobic |
| C25 | CE | MET- 213 | 4.2 | 0 | Hydrophobic |
| C3 | CE | MET- 213 | 3.3 | 0 | Hydrophobic |
| C8 | C3N | NAP- 1269 | 4.18 | 0 | Hydrophobic |
| N16 | O2A | NAP- 1269 | 2.89 | 155.59 | H-Bond (Ligand Donor) |
| N19 | O2A | NAP- 1269 | 3.09 | 140.74 | H-Bond (Ligand Donor) |
| N18 | O2D | NAP- 1269 | 2.78 | 152.13 | H-Bond (Protein Donor) |
