sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Å
NMR
1997-07-22
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_LACCA |
| AC: | P00381 |
| Organism: | Lactobacillus casei |
| Reign: | Bacteria |
| TaxID: | 1582 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 0.000 |
|---|---|
| Number of residues: | 35 |
| Including | |
| Standard Amino Acids: | 35 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.241 | 1022.625 |
| % Hydrophobic | % Polar |
|---|---|
| 52.81 | 47.19 |
| According to VolSite | |
| HET Code: | MTX |
|---|---|
| Formula: | C20H20N8O5 |
| Molecular weight: | 452.423 g/mol |
| DrugBank ID: | DB00563 |
| Buried Surface Area: | 47.01 % |
| Polar Surface area: | 216.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 12 |
| H-Bond Donors: | 3 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| 132.383 | 3.53103 | 7.38567 |
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 |
| NA4 | O | LEU- 4 | 2.93 | 126.17 | H-Bond (Ligand Donor) |
| CM | CD1 | LEU- 19 | 4.49 | 0 | Hydrophobic |
| NA2 | OD2 | ASP- 26 | 3.22 | 173.09 | H-Bond (Ligand Donor) |
| C13 | CD2 | LEU- 27 | 3.84 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 27 | 3.52 | 0 | Hydrophobic |
| CB | CB | ARG- 31 | 4.2 | 0 | Hydrophobic |
| C9 | CG2 | THR- 45 | 4.47 | 0 | Hydrophobic |
| CM | CB | SER- 48 | 4.39 | 0 | Hydrophobic |
| C9 | CE1 | PHE- 49 | 3.91 | 0 | Hydrophobic |
| CM | CE1 | PHE- 49 | 4.39 | 0 | Hydrophobic |
| O1 | NH1 | ARG- 57 | 3.27 | 158.18 | H-Bond (Protein Donor) |
| O1 | NH2 | ARG- 57 | 3.45 | 147.44 | H-Bond (Protein Donor) |
| O2 | NH2 | ARG- 57 | 3.14 | 140.21 | H-Bond (Protein Donor) |
| O1 | CZ | ARG- 57 | 3.82 | 0 | Ionic (Protein Cationic) |
| O2 | CZ | ARG- 57 | 3.99 | 0 | Ionic (Protein Cationic) |
