sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.760 Å
X-ray
2013-04-26
| 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: | 13.500 |
|---|---|
| Number of residues: | 36 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 2 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 1.157 | 691.875 |
| % Hydrophobic | % Polar |
|---|---|
| 64.88 | 35.12 |
| According to VolSite | |
| HET Code: | 1R0 |
|---|---|
| Formula: | C25H23N5O |
| Molecular weight: | 409.483 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 62.65 % |
| Polar Surface area: | 99.94 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 14.505 | 2.13955 | 21.7445 |
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 |
| NAD | O | ILE- 7 | 3.31 | 157.4 | H-Bond (Ligand Donor) |
| CAP | CD1 | LEU- 22 | 4.02 | 0 | Hydrophobic |
| N3 | OE2 | GLU- 30 | 2.86 | 175.91 | H-Bond (Ligand Donor) |
| NAC | OE1 | GLU- 30 | 2.82 | 175.12 | H-Bond (Ligand Donor) |
| CAA | CD1 | PHE- 31 | 4.05 | 0 | Hydrophobic |
| CBE | CE1 | PHE- 31 | 3.02 | 0 | Hydrophobic |
| CAA | CB | PHE- 34 | 3.77 | 0 | Hydrophobic |
| CAF | CE1 | PHE- 34 | 4.19 | 0 | Hydrophobic |
| CAI | CE2 | PHE- 34 | 2.83 | 0 | Hydrophobic |
| CAO | CG2 | ILE- 60 | 4.48 | 0 | Hydrophobic |
| CAK | CG2 | ILE- 60 | 4.46 | 0 | Hydrophobic |
| CAN | CG1 | ILE- 60 | 4.3 | 0 | Hydrophobic |
| CAB | CG | PRO- 61 | 3.9 | 0 | Hydrophobic |
| CAK | CB | ASN- 64 | 4.07 | 0 | Hydrophobic |
| CAG | CD2 | LEU- 67 | 3.23 | 0 | Hydrophobic |
| CAQ | C5N | NDP- 201 | 4.22 | 0 | Hydrophobic |
| CAE | C4N | NDP- 201 | 3.82 | 0 | Hydrophobic |
