sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.700 Å
X-ray
2011-07-07
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.120 | 9.120 | 9.120 | 0.000 | 9.120 | 1 |
| Name: | Dihydrofolate reductase |
|---|---|
| ID: | DYR_STAAU |
| AC: | P0A017 |
| Organism: | Staphylococcus aureus |
| Reign: | Bacteria |
| TaxID: | 1280 |
| EC Number: | 1.5.1.3 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| X | 100 % |
| B-Factor: | 15.315 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 27 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | NAP |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.378 | 361.125 |
| % Hydrophobic | % Polar |
|---|---|
| 72.90 | 27.10 |
| According to VolSite | |
| HET Code: | M23 |
|---|---|
| Formula: | C17H17BrN4O |
| Molecular weight: | 373.247 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.99 % |
| Polar Surface area: | 87.05 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -4.84461 | 31.7861 | -6.2597 |
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 |
| N11 | O | LEU- 6 | 2.74 | 170.73 | H-Bond (Ligand Donor) |
| C15 | CG | LEU- 21 | 3.83 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 21 | 4.48 | 0 | Hydrophobic |
| C22 | CG | LEU- 21 | 3.69 | 0 | Hydrophobic |
| C10 | CD1 | LEU- 21 | 3.94 | 0 | Hydrophobic |
| N4 | OD2 | ASP- 28 | 2.75 | 162.92 | H-Bond (Ligand Donor) |
| N12 | OD1 | ASP- 28 | 2.78 | 164.79 | H-Bond (Ligand Donor) |
| N12 | OD2 | ASP- 28 | 3.21 | 135.24 | H-Bond (Ligand Donor) |
| C19 | CD1 | LEU- 29 | 3.49 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 29 | 3.49 | 0 | Hydrophobic |
| C6 | CG2 | VAL- 32 | 4.4 | 0 | Hydrophobic |
| C10 | CG2 | VAL- 32 | 4.48 | 0 | Hydrophobic |
| C13 | CG2 | THR- 47 | 3.71 | 0 | Hydrophobic |
| C23 | CG2 | THR- 47 | 4.34 | 0 | Hydrophobic |
| C23 | CB | SER- 50 | 3.61 | 0 | Hydrophobic |
| C13 | CG2 | ILE- 51 | 3.8 | 0 | Hydrophobic |
| C16 | CG2 | ILE- 51 | 3.82 | 0 | Hydrophobic |
| BR | CD2 | LEU- 55 | 4.4 | 0 | Hydrophobic |
| N11 | O | PHE- 93 | 2.8 | 148.2 | H-Bond (Ligand Donor) |
| C13 | CE2 | PHE- 93 | 3.39 | 0 | Hydrophobic |
| C7 | CZ | PHE- 93 | 3.35 | 0 | Hydrophobic |
| C13 | C5N | NAP- 169 | 4 | 0 | Hydrophobic |
| C23 | C2D | NAP- 169 | 3.47 | 0 | Hydrophobic |
| N12 | O | HOH- 181 | 3.1 | 142.81 | H-Bond (Ligand Donor) |
