sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2012-07-23
| 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 |
|---|---|
| X | 100 % |
| B-Factor: | 23.888 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.299 | 428.625 |
| % Hydrophobic | % Polar |
|---|---|
| 63.78 | 36.22 |
| According to VolSite | |
| HET Code: | TOP |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB00440 |
| Buried Surface Area: | 68.48 % |
| 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 |
|---|---|---|
| -4.80724 | 0.692524 | 11.8381 |
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 | 2.72 | 167.63 | H-Bond (Ligand Donor) |
| C20 | CG | LEU- 25 | 3.8 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 25 | 3.89 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 25 | 3.66 | 0 | Hydrophobic |
| N2 | OE2 | GLU- 32 | 3.5 | 124.69 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 32 | 3.04 | 174.63 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 32 | 2.62 | 172.87 | H-Bond (Ligand Donor) |
| C14 | CG2 | ILE- 33 | 4.19 | 0 | Hydrophobic |
| C12 | CD1 | ILE- 33 | 4.15 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 36 | 3.89 | 0 | Hydrophobic |
| C14 | CE2 | PHE- 36 | 3.73 | 0 | Hydrophobic |
| C20 | CB | SER- 64 | 3.88 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 65 | 4.03 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 72 | 4.27 | 0 | Hydrophobic |
| N7 | O | ILE- 123 | 2.67 | 147.62 | H-Bond (Ligand Donor) |
| C9 | C4N | NDP- 302 | 3.67 | 0 | Hydrophobic |
| C20 | C2D | NDP- 302 | 3.69 | 0 | Hydrophobic |
