sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.150 Å
X-ray
2009-10-09
| Name: | Peptide deformylase |
|---|---|
| ID: | DEF_ECOLI |
| AC: | P0A6K3 |
| Organism: | Escherichia coli |
| Reign: | Bacteria |
| TaxID: | 83333 |
| EC Number: | 3.5.1.88 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 94 % |
| C | 6 % |
| B-Factor: | 34.438 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 31 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.597 | 793.125 |
| % Hydrophobic | % Polar |
|---|---|
| 45.53 | 54.47 |
| According to VolSite | |
| HET Code: | 2BB |
|---|---|
| Formula: | C16H31N3O5 |
| Molecular weight: | 345.434 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.32 % |
| Polar Surface area: | 118.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -33.3579 | 7.73529 | -16.107 |
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 |
| C14 | CB | GLU- 42 | 4 | 0 | Hydrophobic |
| C1 | CD1 | ILE- 44 | 3.8 | 0 | Hydrophobic |
| C4 | CG1 | ILE- 44 | 4.26 | 0 | Hydrophobic |
| O4 | N | ILE- 44 | 2.72 | 133.65 | H-Bond (Protein Donor) |
| C3 | CB | GLU- 88 | 3.58 | 0 | Hydrophobic |
| O5 | N | GLY- 89 | 2.98 | 166.6 | H-Bond (Protein Donor) |
| O2 | N | LEU- 91 | 3.06 | 157.64 | H-Bond (Protein Donor) |
| C16 | CD | ARG- 97 | 3.86 | 0 | Hydrophobic |
| C1 | CG2 | ILE- 128 | 4.32 | 0 | Hydrophobic |
| C1 | CB | CYS- 129 | 3.78 | 0 | Hydrophobic |
| C4 | SG | CYS- 129 | 4.37 | 0 | Hydrophobic |
| C1 | CB | HIS- 132 | 4.43 | 0 | Hydrophobic |
| C3 | CB | HIS- 132 | 4.48 | 0 | Hydrophobic |
| O3 | OE1 | GLU- 133 | 2.76 | 127.08 | H-Bond (Protein Donor) |
