sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
1999-03-18
| 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: | 18.262 |
|---|---|
| Number of residues: | 33 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.559 | 1069.875 |
| % Hydrophobic | % Polar |
|---|---|
| 58.99 | 41.01 |
| According to VolSite | |
| HET Code: | FOL |
|---|---|
| Formula: | C19H17N7O6 |
| Molecular weight: | 439.382 g/mol |
| DrugBank ID: | DB00158 |
| Buried Surface Area: | 54.86 % |
| 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 |
|---|---|---|
| 8.75203 | 53.5835 | 33.5504 |
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 | OE2 | GLU- 32 | 2.94 | 174.67 | H-Bond (Ligand Donor) |
| N3 | OE1 | GLU- 32 | 2.71 | 172.53 | H-Bond (Ligand Donor) |
| CG | CG1 | ILE- 33 | 4.1 | 0 | Hydrophobic |
| C16 | CD1 | ILE- 33 | 3.54 | 0 | Hydrophobic |
| CB | CD | LYS- 37 | 4.37 | 0 | Hydrophobic |
| O1 | NZ | LYS- 37 | 2.96 | 155.82 | H-Bond (Protein Donor) |
| O1 | NZ | LYS- 37 | 2.96 | 0 | Ionic (Protein Cationic) |
| C9 | CG2 | THR- 61 | 3.85 | 0 | Hydrophobic |
| C12 | CG1 | ILE- 65 | 4.04 | 0 | Hydrophobic |
| CB | CD1 | PHE- 69 | 4.48 | 0 | Hydrophobic |
| CG | CE1 | PHE- 69 | 4.03 | 0 | Hydrophobic |
| O1 | CZ | ARG- 75 | 3.73 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 75 | 3.49 | 0 | Ionic (Protein Cationic) |
| O1 | NH2 | ARG- 75 | 2.88 | 169.42 | H-Bond (Protein Donor) |
| O2 | NH1 | ARG- 75 | 2.79 | 162.04 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 75 | 3.44 | 127.7 | H-Bond (Protein Donor) |
| O1 | O | HOH- 215 | 2.91 | 179.97 | H-Bond (Protein Donor) |
