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
2009-04-21
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.000 | 7.000 | 7.000 | 0.000 | 7.000 | 1 |
| 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 |
|---|---|
| E | 97 % |
| H | 3 % |
| B-Factor: | 15.246 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.795 | 556.875 |
| % Hydrophobic | % Polar |
|---|---|
| 60.61 | 39.39 |
| According to VolSite | |
| HET Code: | DVP |
|---|---|
| Formula: | C21H24N8O3 |
| Molecular weight: | 436.467 g/mol |
| DrugBank ID: | DB07689 |
| Buried Surface Area: | 49.28 % |
| Polar Surface area: | 162.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 7.79341 | 25.4548 | 103.274 |
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 |
| N2 | O | SER- 111 | 2.96 | 124.02 | H-Bond (Ligand Donor) |
| N2 | OG | SER- 111 | 2.65 | 151.96 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 113 | 3.8 | 0 | Aromatic Face/Face |
| CAY | CG | PRO- 115 | 4.44 | 0 | Hydrophobic |
| CAI | CG | LEU- 188 | 4.48 | 0 | Hydrophobic |
| CAS | CD1 | LEU- 188 | 3.97 | 0 | Hydrophobic |
| CAR | CD2 | LEU- 188 | 3.74 | 0 | Hydrophobic |
| CAI | CE1 | TYR- 191 | 3.54 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 226 | 3.91 | 0 | Hydrophobic |
| CAQ | CD2 | LEU- 226 | 4.2 | 0 | Hydrophobic |
| CAC | CD1 | LEU- 229 | 4.35 | 0 | Hydrophobic |
| C9 | C4N | NAP- 300 | 3.96 | 0 | Hydrophobic |
| N2 | O1A | NAP- 300 | 3.26 | 129.45 | H-Bond (Ligand Donor) |
| N3 | O1A | NAP- 300 | 2.68 | 158.74 | H-Bond (Ligand Donor) |
