sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.450 Å
X-ray
2013-01-25
| Name: | Isopenicillin N synthase |
|---|---|
| ID: | IPNS_EMENI |
| AC: | P05326 |
| Organism: | Emericella nidulans |
| Reign: | Eukaryota |
| TaxID: | 227321 |
| EC Number: | 1.21.3.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 10.542 |
|---|---|
| Number of residues: | 41 |
| Including | |
| Standard Amino Acids: | 39 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE |
| Ligandability | Volume (Å3) |
|---|---|
| 1.577 | 887.625 |
| % Hydrophobic | % Polar |
|---|---|
| 63.12 | 36.88 |
| According to VolSite | |
| HET Code: | WT4 |
|---|---|
| Formula: | C14H24N3O6S2 |
| Molecular weight: | 394.487 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 60.95 % |
| Polar Surface area: | 230.2 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 8 |
| H-Bond Donors: | 4 |
| Rings: | 0 |
| Aromatic rings: | 0 |
| Anionic atoms: | 2 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 13 |
| X | Y | Z |
|---|---|---|
| 10.6847 | 38.3246 | 4.93768 |
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 |
| O2 | NH2 | ARG- 87 | 3.04 | 170.85 | H-Bond (Protein Donor) |
| O3 | NE | ARG- 87 | 3.06 | 168.41 | H-Bond (Protein Donor) |
| O2 | CZ | ARG- 87 | 3.9 | 0 | Ionic (Protein Cationic) |
| O3 | CZ | ARG- 87 | 3.87 | 0 | Ionic (Protein Cationic) |
| O2 | OG | SER- 183 | 2.83 | 170.24 | H-Bond (Protein Donor) |
| C11 | CG2 | VAL- 185 | 4.25 | 0 | Hydrophobic |
| O4 | OH | TYR- 189 | 2.55 | 159.17 | H-Bond (Protein Donor) |
| C5 | CZ | PHE- 211 | 3.54 | 0 | Hydrophobic |
| C | CD2 | LEU- 231 | 3.25 | 0 | Hydrophobic |
| C | CG2 | VAL- 272 | 3.67 | 0 | Hydrophobic |
| O5 | OG | SER- 281 | 2.75 | 168.82 | H-Bond (Protein Donor) |
| S1 | CZ | PHE- 285 | 3.64 | 0 | Hydrophobic |
| C10 | CD2 | LEU- 321 | 3.7 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 324 | 3.72 | 0 | Hydrophobic |
| C8 | CG2 | THR- 331 | 4.41 | 0 | Hydrophobic |
| O5 | O | HOH- 2181 | 2.76 | 179.96 | H-Bond (Protein Donor) |
