sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.260 Å
X-ray
2013-08-05
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_MYCTU |
| AC: | P9WNX1 |
| Organism: | Mycobacterium tuberculosis |
| Reign: | Bacteria |
| TaxID: | 83332 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 28.874 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | NDP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.808 | 506.250 |
| % Hydrophobic | % Polar |
|---|---|
| 58.00 | 42.00 |
| According to VolSite | |
| HET Code: | TMQ |
|---|---|
| Formula: | C19H23N5O3 |
| Molecular weight: | 369.418 g/mol |
| DrugBank ID: | DB01157 |
| Buried Surface Area: | 60.42 % |
| Polar Surface area: | 117.54 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 3.38522 | -7.14659 | 2.07696 |
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 |
| N25 | O | ILE- 5 | 2.86 | 142.4 | H-Bond (Ligand Donor) |
| C8 | CD1 | ILE- 20 | 3.9 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 20 | 4.23 | 0 | Hydrophobic |
| C7 | CD1 | ILE- 20 | 3.26 | 0 | Hydrophobic |
| N1 | OD1 | ASP- 27 | 3.27 | 129.71 | H-Bond (Ligand Donor) |
| N1 | OD2 | ASP- 27 | 2.62 | 171.03 | H-Bond (Ligand Donor) |
| N24 | OD1 | ASP- 27 | 2.74 | 158.09 | H-Bond (Ligand Donor) |
| C22 | CG | GLN- 28 | 4.44 | 0 | Hydrophobic |
| C17 | CE1 | PHE- 31 | 4.04 | 0 | Hydrophobic |
| C23 | CE2 | PHE- 31 | 3.92 | 0 | Hydrophobic |
| C17 | CG2 | THR- 46 | 4.3 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 50 | 3.65 | 0 | Hydrophobic |
| C16 | CD2 | LEU- 50 | 3.99 | 0 | Hydrophobic |
| C14 | CG | PRO- 51 | 3.83 | 0 | Hydrophobic |
| C21 | CG | PRO- 51 | 3.66 | 0 | Hydrophobic |
| C13 | CG | PRO- 51 | 3.41 | 0 | Hydrophobic |
| C15 | CG2 | VAL- 54 | 4.24 | 0 | Hydrophobic |
| C22 | CG1 | VAL- 54 | 4.41 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 57 | 3.92 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 94 | 3.75 | 0 | Hydrophobic |
| N25 | O | ILE- 94 | 2.86 | 132.02 | H-Bond (Ligand Donor) |
| N24 | OG1 | THR- 113 | 3.36 | 128.7 | H-Bond (Ligand Donor) |
| C6 | C4N | NDP- 201 | 4.16 | 0 | Hydrophobic |
| C9 | C5N | NDP- 201 | 4.5 | 0 | Hydrophobic |
| C17 | C4N | NDP- 201 | 3.36 | 0 | Hydrophobic |
| C5 | C4N | NDP- 201 | 3.45 | 0 | Hydrophobic |
