sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
1999-03-15
| 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: | 25.427 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.316 | 475.875 |
| % Hydrophobic | % Polar |
|---|---|
| 73.05 | 26.95 |
| According to VolSite | |
| HET Code: | FOL |
|---|---|
| Formula: | C19H17N7O6 |
| Molecular weight: | 439.382 g/mol |
| DrugBank ID: | DB00158 |
| Buried Surface Area: | 64.52 % |
| Polar Surface area: | 214.64 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| 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 |
|---|---|---|
| 13.4876 | 6.65712 | 9.98366 |
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 |
| C13 | CD2 | LEU- 25 | 3.78 | 0 | Hydrophobic |
| NA2 | OE2 | GLU- 32 | 2.78 | 178.4 | H-Bond (Ligand Donor) |
| N3 | OE1 | GLU- 32 | 2.83 | 173.87 | H-Bond (Ligand Donor) |
| CB | CG2 | ILE- 33 | 3.97 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 33 | 3.68 | 0 | Hydrophobic |
| CB | CD | LYS- 37 | 3.8 | 0 | Hydrophobic |
| O2 | NZ | LYS- 37 | 2.65 | 170.64 | H-Bond (Protein Donor) |
| O2 | NZ | LYS- 37 | 2.65 | 0 | Ionic (Protein Cationic) |
| C9 | CG2 | THR- 61 | 3.93 | 0 | Hydrophobic |
| C14 | CG1 | ILE- 65 | 4.38 | 0 | Hydrophobic |
| CG | CD1 | PHE- 69 | 3.38 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 72 | 4.09 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 75 | 3.12 | 158.98 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 75 | 3.08 | 162.77 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 75 | 3.83 | 0 | Ionic (Protein Cationic) |
| C9 | C4N | NAP- 207 | 3.45 | 0 | Hydrophobic |
| NA2 | O | HOH- 215 | 3.28 | 135.95 | H-Bond (Ligand Donor) |
