sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.610 Å
X-ray
2007-07-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 7.430 | 7.430 | 7.430 | 0.000 | 7.430 | 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 |
|---|---|
| A | 96 % |
| D | 4 % |
| B-Factor: | 18.102 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.162 | 536.625 |
| % Hydrophobic | % Polar |
|---|---|
| 50.31 | 49.69 |
| According to VolSite | |
| HET Code: | FE1 |
|---|---|
| Formula: | C22H26N8O3 |
| Molecular weight: | 450.494 g/mol |
| DrugBank ID: | DB07765 |
| Buried Surface Area: | 47.84 % |
| Polar Surface area: | 153.44 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 10 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -7.68021 | 32.2326 | 66.8538 |
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 | 3.05 | 121.27 | H-Bond (Ligand Donor) |
| N2 | OG | SER- 111 | 2.91 | 160.04 | H-Bond (Ligand Donor) |
| DuAr | DuAr | PHE- 113 | 3.79 | 0 | Aromatic Face/Face |
| CAS | CD2 | LEU- 188 | 3.65 | 0 | Hydrophobic |
| N4 | OH | TYR- 194 | 2.77 | 174.17 | H-Bond (Ligand Donor) |
| CAB | CD2 | LEU- 226 | 3.61 | 0 | Hydrophobic |
| CAJ | CD2 | LEU- 226 | 4.41 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 229 | 3.67 | 0 | Hydrophobic |
| CAK | CD1 | LEU- 229 | 4.1 | 0 | Hydrophobic |
| CAB | C4N | NAP- 1300 | 4.14 | 0 | Hydrophobic |
| N1 | O1A | NAP- 1300 | 2.9 | 159.83 | H-Bond (Ligand Donor) |
| N2 | O1A | NAP- 1300 | 3.39 | 134.46 | H-Bond (Ligand Donor) |
