sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2009-08-04
| Name: | Methylenetetrahydrofolate reductase |
|---|---|
| ID: | A3DHS7_CLOTH |
| AC: | A3DHS7 |
| Organism: | Clostridium thermocellum |
| Reign: | Bacteria |
| TaxID: | 203119 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 44.122 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.095 | 698.625 |
| % Hydrophobic | % Polar |
|---|---|
| 59.90 | 40.10 |
| According to VolSite | |
| HET Code: | C2F |
|---|---|
| Formula: | C20H23N7O6 |
| Molecular weight: | 457.440 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 47.42 % |
| Polar Surface area: | 204.14 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 11 |
| H-Bond Donors: | 5 |
| Rings: | 3 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 9 |
| X | Y | Z |
|---|---|---|
| -40.5022 | -34.0086 | 39.2296 |
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 |
| C6 | CG2 | THR- 19 | 3.94 | 0 | Hydrophobic |
| C7 | CB | THR- 19 | 3.58 | 0 | Hydrophobic |
| C11 | CG2 | THR- 19 | 4.33 | 0 | Hydrophobic |
| C16 | CB | PRO- 21 | 4.12 | 0 | Hydrophobic |
| C11 | CG | LYS- 22 | 4.31 | 0 | Hydrophobic |
| O | NZ | LYS- 29 | 3.5 | 137.66 | H-Bond (Protein Donor) |
| C16 | CD1 | ILE- 33 | 4.05 | 0 | Hydrophobic |
| C17 | CG1 | ILE- 33 | 3.63 | 0 | Hydrophobic |
| O2 | NH2 | ARG- 40 | 3.31 | 142.06 | H-Bond (Protein Donor) |
| C11 | CD1 | ILE- 70 | 3.52 | 0 | Hydrophobic |
| C7 | CE2 | PHE- 227 | 4.06 | 0 | Hydrophobic |
| N8 | O | VAL- 282 | 3.04 | 162.19 | H-Bond (Ligand Donor) |
| C9 | CG1 | VAL- 284 | 4.21 | 0 | Hydrophobic |
| C15 | CG1 | VAL- 284 | 3.78 | 0 | Hydrophobic |
| CG | CB | LYS- 286 | 3.56 | 0 | Hydrophobic |
| OE1 | N | LYS- 286 | 3.33 | 145.81 | H-Bond (Protein Donor) |
| C13 | CD1 | ILE- 289 | 4.21 | 0 | Hydrophobic |
