sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.350 Å
X-ray
2010-07-06
| 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: | 16.787 |
|---|---|
| Number of residues: | 40 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 2 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.881 | 553.500 |
| % Hydrophobic | % Polar |
|---|---|
| 52.44 | 47.56 |
| According to VolSite | |
| HET Code: | 3TZ |
|---|---|
| Formula: | C23H19N5O6S |
| Molecular weight: | 493.492 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.97 % |
| Polar Surface area: | 217.11 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 9 |
| H-Bond Donors: | 4 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -0.8562 | 14.4817 | 25.1985 |
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 |
| SAV | CG2 | ILE- 7 | 4.34 | 0 | Hydrophobic |
| CAQ | CD1 | LEU- 22 | 3.89 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 30 | 2.82 | 174.56 | H-Bond (Ligand Donor) |
| NAA | OE1 | GLU- 30 | 2.85 | 178.39 | H-Bond (Ligand Donor) |
| CG | CB | PHE- 31 | 4.25 | 0 | Hydrophobic |
| CAJ | CB | PHE- 31 | 3.68 | 0 | Hydrophobic |
| CAJ | CB | PHE- 34 | 4.48 | 0 | Hydrophobic |
| SAV | CE1 | PHE- 34 | 3.41 | 0 | Hydrophobic |
| CB | CB | GLN- 35 | 3.98 | 0 | Hydrophobic |
| CAH | CG2 | THR- 56 | 3.53 | 0 | Hydrophobic |
| CAM | CG2 | ILE- 60 | 4.14 | 0 | Hydrophobic |
| CAH | CG1 | ILE- 60 | 4.06 | 0 | Hydrophobic |
| O | CZ | ARG- 70 | 3.88 | 0 | Ionic (Protein Cationic) |
| OXT | CZ | ARG- 70 | 3.5 | 0 | Ionic (Protein Cationic) |
| O | NH2 | ARG- 70 | 2.88 | 163.02 | H-Bond (Protein Donor) |
| OXT | NH1 | ARG- 70 | 2.89 | 156.9 | H-Bond (Protein Donor) |
| OXT | NH2 | ARG- 70 | 3.29 | 135.27 | H-Bond (Protein Donor) |
| SAV | CB | VAL- 115 | 3.94 | 0 | Hydrophobic |
| CAN | CB | VAL- 115 | 3.81 | 0 | Hydrophobic |
| SAV | C4N | NDP- 188 | 3.6 | 0 | Hydrophobic |
| O6 | O | HOH- 252 | 2.92 | 162.51 | H-Bond (Protein Donor) |
| O | O | HOH- 357 | 3.03 | 146.67 | H-Bond (Protein Donor) |
