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
2009-02-05
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 9.520 | 9.520 | 9.520 | 0.000 | 9.520 | 1 |
| Name: | Peptide deformylase, mitochondrial |
|---|---|
| ID: | DEFM_HUMAN |
| AC: | Q9HBH1 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 3.5.1.88 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 12.401 |
|---|---|
| Number of residues: | 28 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 0.438 | 617.625 |
| % Hydrophobic | % Polar |
|---|---|
| 39.34 | 60.66 |
| According to VolSite | |
| HET Code: | BB2 |
|---|---|
| Formula: | C19H35N3O5 |
| Molecular weight: | 385.498 g/mol |
| DrugBank ID: | DB04310 |
| Buried Surface Area: | 66.17 % |
| 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 |
|---|---|---|
| 18.3956 | -8.2877 | 27.3236 |
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 |
| C18 | CB | CYS- 50 | 4.27 | 0 | Hydrophobic |
| C5 | CB | CYS- 50 | 3.66 | 0 | Hydrophobic |
| O13 | N | VAL- 51 | 3.1 | 170.39 | H-Bond (Protein Donor) |
| C8 | CG2 | VAL- 51 | 3.58 | 0 | Hydrophobic |
| O2 | NE2 | GLN- 57 | 3.14 | 129.12 | H-Bond (Protein Donor) |
| O27 | NH1 | ARG- 85 | 3.43 | 137.89 | H-Bond (Protein Donor) |
| C24 | CE | MET- 87 | 4.33 | 0 | Hydrophobic |
| C11 | CG | GLU- 112 | 3.77 | 0 | Hydrophobic |
| C10 | CG | GLU- 112 | 3.53 | 0 | Hydrophobic |
| N14 | O | GLY- 113 | 3.41 | 171.21 | H-Bond (Ligand Donor) |
| O20 | N | GLY- 113 | 2.88 | 151.67 | H-Bond (Protein Donor) |
| C5 | CG | GLU- 115 | 3.82 | 0 | Hydrophobic |
| O4 | N | GLU- 115 | 3 | 157.93 | H-Bond (Protein Donor) |
| C17 | CD2 | LEU- 121 | 4.33 | 0 | Hydrophobic |
| C26 | CD2 | LEU- 121 | 3.78 | 0 | Hydrophobic |
| C11 | CZ2 | TRP- 149 | 3.44 | 0 | Hydrophobic |
| C25 | CZ2 | TRP- 149 | 3.47 | 0 | Hydrophobic |
| C10 | CG | ARG- 152 | 3.65 | 0 | Hydrophobic |
| C11 | CD | ARG- 152 | 3.62 | 0 | Hydrophobic |
| C7 | CG2 | ILE- 153 | 4.39 | 0 | Hydrophobic |
| C8 | CG1 | ILE- 153 | 4.01 | 0 | Hydrophobic |
| C10 | CG1 | ILE- 153 | 4.17 | 0 | Hydrophobic |
| C9 | CB | HIS- 156 | 3.91 | 0 | Hydrophobic |
| N1 | OE2 | GLU- 157 | 2.63 | 126.74 | H-Bond (Ligand Donor) |
| O2 | OE1 | GLU- 157 | 2.62 | 144.54 | H-Bond (Protein Donor) |
