sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.860 Å
X-ray
1994-09-14
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.820 | 6.820 | 6.820 | 0.000 | 6.820 | 2 |
| 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: | 17.465 |
|---|---|
| Number of residues: | 27 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.467 | 354.375 |
| % Hydrophobic | % Polar |
|---|---|
| 76.19 | 23.81 |
| According to VolSite | |
| HET Code: | TOP |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB00440 |
| Buried Surface Area: | 66.31 % |
| Polar Surface area: | 105.51 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 5 |
| X | Y | Z |
|---|---|---|
| 17.4391 | 5.64443 | -6.501 |
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 |
| N7 | O | ILE- 10 | 2.9 | 164.96 | H-Bond (Ligand Donor) |
| C14 | CD1 | LEU- 25 | 3.83 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 25 | 3.69 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 32 | 2.84 | 159.87 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 32 | 2.65 | 169.26 | H-Bond (Ligand Donor) |
| N4 | OE1 | GLU- 32 | 3.41 | 130.35 | H-Bond (Ligand Donor) |
| C17 | CD1 | ILE- 33 | 4.07 | 0 | Hydrophobic |
| C20 | CG2 | ILE- 33 | 4.04 | 0 | Hydrophobic |
| C18 | CD1 | ILE- 33 | 3.87 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 36 | 3.98 | 0 | Hydrophobic |
| C20 | CE2 | PHE- 36 | 3.83 | 0 | Hydrophobic |
| C14 | CB | SER- 64 | 4.2 | 0 | Hydrophobic |
| C15 | CG1 | ILE- 65 | 3.91 | 0 | Hydrophobic |
| C17 | CG | PRO- 66 | 4.3 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 69 | 4.29 | 0 | Hydrophobic |
| C20 | CD2 | LEU- 72 | 4.39 | 0 | Hydrophobic |
| N7 | O | ILE- 123 | 2.9 | 136.07 | H-Bond (Ligand Donor) |
| C9 | C4N | NDP- 391 | 3.76 | 0 | Hydrophobic |
| C14 | C2D | NDP- 391 | 3.91 | 0 | Hydrophobic |
