sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.400 Å
X-ray
2010-03-16
| Name: | Peptide deformylase 1B, chloroplastic/mitochondrial |
|---|---|
| ID: | DEF1B_ARATH |
| AC: | Q9FUZ2 |
| Organism: | Arabidopsis thaliana |
| Reign: | Eukaryota |
| TaxID: | 3702 |
| EC Number: | 3.5.1.88 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 31.833 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | ZN |
| Ligandability | Volume (Å3) |
|---|---|
| 0.347 | 243.000 |
| % Hydrophobic | % Polar |
|---|---|
| 51.39 | 48.61 |
| According to VolSite | |
| HET Code: | BB2 |
|---|---|
| Formula: | C19H35N3O5 |
| Molecular weight: | 385.498 g/mol |
| DrugBank ID: | DB04310 |
| Buried Surface Area: | 64.08 % |
| Polar Surface area: | 118.97 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 1 |
| Aromatic rings: | 0 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 1.84011 | -20.1276 | -30.7253 |
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 |
| C5 | CG | GLN- 41 | 3.83 | 0 | Hydrophobic |
| C6 | CB | GLN- 41 | 4.43 | 0 | Hydrophobic |
| O13 | N | ILE- 42 | 3.05 | 157.12 | H-Bond (Protein Donor) |
| C24 | CD1 | ILE- 42 | 4.37 | 0 | Hydrophobic |
| C11 | CD1 | ILE- 42 | 3.63 | 0 | Hydrophobic |
| O4 | NE2 | GLN- 48 | 2.8 | 169.69 | H-Bond (Protein Donor) |
| C26 | CE1 | PHE- 87 | 4.34 | 0 | Hydrophobic |
| O27 | O | ASP- 88 | 2.86 | 143.62 | H-Bond (Ligand Donor) |
| C10 | CG | GLU- 89 | 4.22 | 0 | Hydrophobic |
| N14 | O | GLY- 90 | 3.44 | 164.22 | H-Bond (Ligand Donor) |
| O20 | N | GLY- 90 | 3.07 | 165.43 | H-Bond (Protein Donor) |
| C5 | CB | LEU- 92 | 4.12 | 0 | Hydrophobic |
| O4 | N | LEU- 92 | 2.79 | 162.54 | H-Bond (Protein Donor) |
| C17 | CE1 | TYR- 98 | 3.34 | 0 | Hydrophobic |
| C11 | CG | ARG- 129 | 3.98 | 0 | Hydrophobic |
| C9 | CG2 | ILE- 130 | 3.63 | 0 | Hydrophobic |
| C11 | CG1 | ILE- 130 | 4.08 | 0 | Hydrophobic |
| C10 | CB | HIS- 133 | 3.73 | 0 | Hydrophobic |
| O4 | ZN | ZN- 195 | 2.3 | 0 | Metal Acceptor |
| O2 | ZN | ZN- 195 | 2.34 | 0 | Metal Acceptor |
