sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2001-12-12
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_PNECA |
| AC: | P16184 |
| Organism: | Pneumocystis carinii |
| Reign: | Eukaryota |
| TaxID: | 4754 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 35.233 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.542 | 570.375 |
| % Hydrophobic | % Polar |
|---|---|
| 65.68 | 34.32 |
| According to VolSite | |
| HET Code: | PMD |
|---|---|
| Formula: | C21H17N7 |
| Molecular weight: | 367.407 g/mol |
| DrugBank ID: | DB08406 |
| Buried Surface Area: | 62.1 % |
| Polar Surface area: | 106.84 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 2 |
| X | Y | Z |
|---|---|---|
| 15.1849 | 5.55554 | 11.7006 |
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 |
| N4' | O | ILE- 10 | 2.84 | 164.18 | H-Bond (Ligand Donor) |
| C3' | CB | SER- 24 | 4.39 | 0 | Hydrophobic |
| C9B | CD1 | LEU- 25 | 3.73 | 0 | Hydrophobic |
| C0' | CD1 | LEU- 25 | 4.1 | 0 | Hydrophobic |
| C1' | CG | LEU- 25 | 3.99 | 0 | Hydrophobic |
| N1' | OE1 | GLU- 32 | 2.66 | 170.05 | H-Bond (Ligand Donor) |
| N2' | OE2 | GLU- 32 | 2.84 | 163.57 | H-Bond (Ligand Donor) |
| CA' | CE2 | PHE- 36 | 3.42 | 0 | Hydrophobic |
| C3' | CB | SER- 64 | 3.87 | 0 | Hydrophobic |
| C9' | CD2 | LEU- 72 | 3.85 | 0 | Hydrophobic |
| CA' | CD1 | LEU- 72 | 4.21 | 0 | Hydrophobic |
| N4' | O | ILE- 123 | 2.93 | 124.2 | H-Bond (Ligand Donor) |
| C9B | C4N | NDP- 207 | 4.15 | 0 | Hydrophobic |
| C2' | C2D | NDP- 207 | 3.95 | 0 | Hydrophobic |
