sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.500 Å
X-ray
2008-11-10
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.340 | 5.840 | 5.860 | 1.140 | 8.000 | 9 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_HUMAN |
| AC: | P00374 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 20.293 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.026 | 560.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.43 | 41.57 |
| According to VolSite | |
| HET Code: | TOP |
|---|---|
| Formula: | C14H18N4O3 |
| Molecular weight: | 290.318 g/mol |
| DrugBank ID: | DB00440 |
| Buried Surface Area: | 62.31 % |
| 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 |
|---|---|---|
| 1.91362 | 30.4949 | -2.88438 |
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- 7 | 3.23 | 162.35 | H-Bond (Ligand Donor) |
| C9 | CD2 | LEU- 22 | 4.06 | 0 | Hydrophobic |
| C14 | CD1 | LEU- 22 | 4.13 | 0 | Hydrophobic |
| N2 | OE1 | GLU- 30 | 2.69 | 169.89 | H-Bond (Ligand Donor) |
| N2 | OE2 | GLU- 30 | 3.39 | 132.28 | H-Bond (Ligand Donor) |
| N4 | OE2 | GLU- 30 | 2.82 | 163.77 | H-Bond (Ligand Donor) |
| C14 | CD1 | PHE- 31 | 3.54 | 0 | Hydrophobic |
| C20 | CZ | PHE- 34 | 4.41 | 0 | Hydrophobic |
| C20 | CG2 | THR- 56 | 3.49 | 0 | Hydrophobic |
| C17 | CG2 | ILE- 60 | 3.61 | 0 | Hydrophobic |
| C20 | CD1 | ILE- 60 | 3.8 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 115 | 4 | 0 | Hydrophobic |
| C9 | C3N | NDP- 1188 | 3.58 | 0 | Hydrophobic |
