sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.300 Å
X-ray
2009-03-04
| 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: | 7.650 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.410 | 489.375 |
| % Hydrophobic | % Polar |
|---|---|
| 75.17 | 24.83 |
| According to VolSite | |
| HET Code: | GHC |
|---|---|
| Formula: | C20H18N4O6S2 |
| Molecular weight: | 474.510 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 64.97 % |
| Polar Surface area: | 230.38 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -12.2196 | 8.32056 | -25.4148 |
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 |
| S4 | CG2 | ILE- 7 | 4.39 | 0 | Hydrophobic |
| SAT | CD2 | LEU- 22 | 3.75 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 30 | 2.7 | 164.69 | H-Bond (Ligand Donor) |
| N2 | OE1 | GLU- 30 | 2.73 | 171.61 | H-Bond (Ligand Donor) |
| SAT | CE1 | PHE- 31 | 4.24 | 0 | Hydrophobic |
| CAN | CB | PHE- 31 | 4.33 | 0 | Hydrophobic |
| C29 | CZ | PHE- 34 | 4.05 | 0 | Hydrophobic |
| CAL | CD2 | PHE- 34 | 3.47 | 0 | Hydrophobic |
| S4 | CE1 | PHE- 34 | 3.2 | 0 | Hydrophobic |
| CBG | CD | LYS- 35 | 4.27 | 0 | Hydrophobic |
| C13 | CG2 | THR- 56 | 3.62 | 0 | Hydrophobic |
| C29 | CD1 | ILE- 60 | 4.18 | 0 | Hydrophobic |
| CAK | CG1 | ILE- 60 | 4.33 | 0 | Hydrophobic |
| CBG | CD1 | PHE- 64 | 4.33 | 0 | Hydrophobic |
| CAN | CZ | PHE- 64 | 3.97 | 0 | Hydrophobic |
| OAG | CZ | ARG- 70 | 3.62 | 0 | Ionic (Protein Cationic) |
| OAD | CZ | ARG- 70 | 3.83 | 0 | Ionic (Protein Cationic) |
| OAG | NH2 | ARG- 70 | 3.4 | 135.11 | H-Bond (Protein Donor) |
| OAG | NH1 | ARG- 70 | 2.86 | 162.98 | H-Bond (Protein Donor) |
| OAD | NH2 | ARG- 70 | 2.86 | 156.11 | H-Bond (Protein Donor) |
| C13 | CB | VAL- 115 | 4.2 | 0 | Hydrophobic |
| C29 | CG2 | VAL- 115 | 3.78 | 0 | Hydrophobic |
| S4 | CB | VAL- 115 | 3.92 | 0 | Hydrophobic |
| C13 | C5N | NDP- 188 | 3.49 | 0 | Hydrophobic |
| SAT | C3N | NDP- 188 | 4.29 | 0 | Hydrophobic |
| O6 | O | HOH- 319 | 2.92 | 151.99 | H-Bond (Protein Donor) |
| OAD | O | HOH- 383 | 2.87 | 159.74 | H-Bond (Protein Donor) |
