sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2004-01-13
| 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: | 22.077 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 33 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.433 | 604.125 |
| % Hydrophobic | % Polar |
|---|---|
| 70.95 | 29.05 |
| According to VolSite | |
| HET Code: | TAB |
|---|---|
| Formula: | C23H26ClN7O2 |
| Molecular weight: | 467.951 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.03 % |
| Polar Surface area: | 132.07 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 14.3476 | 6.12806 | 10.8422 |
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 |
| N20 | O | ILE- 10 | 3.22 | 167.3 | H-Bond (Ligand Donor) |
| C20 | CB | ALA- 12 | 4.39 | 0 | Hydrophobic |
| CL8 | CG | LEU- 25 | 4.41 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 25 | 3.52 | 0 | Hydrophobic |
| C20 | CG | LEU- 25 | 4.5 | 0 | Hydrophobic |
| C3' | CD2 | LEU- 25 | 3.67 | 0 | Hydrophobic |
| N17 | OE1 | GLU- 32 | 2.79 | 155.29 | H-Bond (Ligand Donor) |
| N22 | OE2 | GLU- 32 | 2.85 | 155.39 | H-Bond (Ligand Donor) |
| C6' | CD1 | ILE- 33 | 4.5 | 0 | Hydrophobic |
| C22 | CD1 | ILE- 33 | 3.69 | 0 | Hydrophobic |
| C27 | CD1 | ILE- 33 | 4.12 | 0 | Hydrophobic |
| C31 | CG1 | ILE- 33 | 4.19 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 33 | 3.98 | 0 | Hydrophobic |
| C28 | CG1 | ILE- 33 | 3.26 | 0 | Hydrophobic |
| C25 | CG | LYS- 37 | 3.59 | 0 | Hydrophobic |
| CL8 | CG2 | THR- 61 | 3.96 | 0 | Hydrophobic |
| CL8 | CB | SER- 64 | 3.99 | 0 | Hydrophobic |
| CL8 | CG1 | ILE- 65 | 4.41 | 0 | Hydrophobic |
| C19 | CG2 | ILE- 65 | 4.19 | 0 | Hydrophobic |
| C21 | CG2 | ILE- 65 | 4.08 | 0 | Hydrophobic |
| C31 | CG | PRO- 66 | 4.5 | 0 | Hydrophobic |
| C27 | CG | PRO- 66 | 3.76 | 0 | Hydrophobic |
| C29 | CG | PRO- 66 | 3.35 | 0 | Hydrophobic |
| C21 | CB | PHE- 69 | 4.27 | 0 | Hydrophobic |
| C30 | CD1 | PHE- 69 | 3.23 | 0 | Hydrophobic |
| C29 | CB | PHE- 69 | 4.29 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 72 | 4.29 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 72 | 3.88 | 0 | Hydrophobic |
| CL8 | C2D | NDP- 207 | 4.13 | 0 | Hydrophobic |
