sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.450 Å
X-ray
2015-05-07
| Name: | Multidrug transporter MdfA |
|---|---|
| ID: | MDFA_ECOLI |
| AC: | P0AEY8 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 43.386 |
|---|---|
| Number of residues: | 26 |
| Including | |
| Standard Amino Acids: | 26 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.275 | 2457.000 |
| % Hydrophobic | % Polar |
|---|---|
| 48.08 | 51.92 |
| According to VolSite | |
| HET Code: | CLM |
|---|---|
| Formula: | C11H11Cl2N2O5 |
| Molecular weight: | 322.121 g/mol |
| DrugBank ID: | DB00446 |
| Buried Surface Area: | 58.61 % |
| Polar Surface area: | 123.99 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 1 |
| Aromatic rings: | 1 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -17.1977 | 14.3294 | 24.9423 |
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 |
| CL1 | CD1 | TYR- 30 | 3.35 | 0 | Hydrophobic |
| CL2 | CE1 | TYR- 30 | 3.78 | 0 | Hydrophobic |
| CL1 | CB | ASN- 33 | 4.45 | 0 | Hydrophobic |
| O4 | ND2 | ASN- 33 | 2.64 | 140.23 | H-Bond (Protein Donor) |
| O4 | OD2 | ASP- 34 | 3.46 | 144.37 | H-Bond (Ligand Donor) |
| O5 | OD2 | ASP- 34 | 3.03 | 155.81 | H-Bond (Ligand Donor) |
| C4 | CE | MET- 58 | 3.62 | 0 | Hydrophobic |
| CL1 | CE2 | TYR- 61 | 4.25 | 0 | Hydrophobic |
| C1 | CD2 | LEU- 62 | 3.64 | 0 | Hydrophobic |
| CL1 | CD2 | LEU- 119 | 3.75 | 0 | Hydrophobic |
| C8 | CB | ALA- 150 | 4.38 | 0 | Hydrophobic |
| C5 | CB | PRO- 154 | 4.1 | 0 | Hydrophobic |
| C6 | CG | PRO- 154 | 4.04 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 235 | 3.89 | 0 | Hydrophobic |
| C4 | CD2 | LEU- 236 | 4.02 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 236 | 3.64 | 0 | Hydrophobic |
| C4 | CD1 | ILE- 239 | 3.53 | 0 | Hydrophobic |
| C5 | CD1 | ILE- 239 | 4.41 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 239 | 3.93 | 0 | Hydrophobic |
