sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2000-09-11
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.750 | 7.080 | 7.080 | 0.330 | 7.410 | 2 |
| Name: | Pteridine reductase 1 |
|---|---|
| ID: | PTR1_LEIMA |
| AC: | Q01782 |
| Organism: | Leishmania major |
| Reign: | Eukaryota |
| TaxID: | 5664 |
| EC Number: | 1.5.1.33 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 25.971 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.833 | 803.250 |
| % Hydrophobic | % Polar |
|---|---|
| 43.70 | 56.30 |
| According to VolSite | |
| HET Code: | MTX |
|---|---|
| Formula: | C20H20N8O5 |
| Molecular weight: | 452.423 g/mol |
| DrugBank ID: | DB00563 |
| Buried Surface Area: | 51.1 % |
| Polar Surface area: | 216.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 22.4615 | 4.07142 | 13.5173 |
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 |
| NA2 | OG | SER- 111 | 2.78 | 163.43 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 113 | 3.98 | 0 | Aromatic Face/Face |
| C16 | CD2 | LEU- 188 | 3.39 | 0 | Hydrophobic |
| CG | CE1 | TYR- 191 | 4.2 | 0 | Hydrophobic |
| NA4 | OH | TYR- 194 | 2.95 | 167.95 | H-Bond (Ligand Donor) |
| CM | CD2 | LEU- 226 | 3.27 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 229 | 3.51 | 0 | Hydrophobic |
| CM | CD2 | LEU- 229 | 4.08 | 0 | Hydrophobic |
| C13 | CE | MET- 233 | 3.53 | 0 | Hydrophobic |
| N1 | O1A | NDP- 300 | 2.6 | 153.43 | H-Bond (Ligand Donor) |
| NA2 | O1A | NDP- 300 | 3.09 | 131.1 | H-Bond (Ligand Donor) |
| N3 | O2D | NDP- 300 | 2.78 | 156.93 | H-Bond (Protein Donor) |
