sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.000 Å
X-ray
2013-08-13
| Name: | Myeloperoxidase |
|---|---|
| ID: | PERM_HUMAN |
| AC: | P05164 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 1.11.2.2 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 29 % |
| C | 71 % |
| B-Factor: | 9.825 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 30 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 3 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.030 | 1437.750 |
| % Hydrophobic | % Polar |
|---|---|
| 42.72 | 57.28 |
| According to VolSite | |
| HET Code: | NIH |
|---|---|
| Formula: | C14H10F6N4O3 |
| Molecular weight: | 396.245 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.55 % |
| Polar Surface area: | 102.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 4 |
| Rings: | 2 |
| Aromatic rings: | 1 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 17.942 | -19.6905 | -2.55893 |
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 |
| O9 | NE2 | GLN- 91 | 2.9 | 140.68 | H-Bond (Protein Donor) |
| F25 | CE1 | PHE- 99 | 3.91 | 0 | Hydrophobic |
| C20 | CB | PRO- 220 | 4.35 | 0 | Hydrophobic |
| F25 | CB | THR- 238 | 4.24 | 0 | Hydrophobic |
| F26 | CB | THR- 238 | 4.47 | 0 | Hydrophobic |
| O10 | NH1 | ARG- 239 | 2.83 | 162.95 | H-Bond (Protein Donor) |
| F27 | CG | ARG- 239 | 3.36 | 0 | Hydrophobic |
| F23 | CE2 | PHE- 366 | 3.94 | 0 | Hydrophobic |
| C17 | CZ | PHE- 366 | 3.42 | 0 | Hydrophobic |
| F21 | CZ | PHE- 366 | 3.37 | 0 | Hydrophobic |
| F27 | CE1 | PHE- 366 | 3.66 | 0 | Hydrophobic |
| C13 | CE2 | PHE- 407 | 4.16 | 0 | Hydrophobic |
| F23 | CD2 | PHE- 407 | 4.17 | 0 | Hydrophobic |
| F21 | CG2 | VAL- 410 | 4.41 | 0 | Hydrophobic |
| F23 | CG2 | VAL- 410 | 3.76 | 0 | Hydrophobic |
| F23 | SD | MET- 411 | 4.3 | 0 | Hydrophobic |
