sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.010 Å
X-ray
2012-11-21
| Name: | Ferrochelatase, mitochondrial |
|---|---|
| ID: | HEMH_HUMAN |
| AC: | P22830 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 4.99.1.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 19.649 |
|---|---|
| Number of residues: | 30 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.445 | 1107.000 |
| % Hydrophobic | % Polar |
|---|---|
| 60.06 | 39.94 |
| According to VolSite | |
| HET Code: | CHD |
|---|---|
| Formula: | C24H39O5 |
| Molecular weight: | 407.563 g/mol |
| DrugBank ID: | DB02659 |
| Buried Surface Area: | 51.94 % |
| Polar Surface area: | 100.82 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 0 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 4 |
| X | Y | Z |
|---|---|---|
| -6.39476 | -30.4964 | 38.285 |
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 |
| C7 | CE | MET- 76 | 4.17 | 0 | Hydrophobic |
| C15 | SD | MET- 76 | 3.68 | 0 | Hydrophobic |
| C6 | CE2 | PHE- 88 | 4.02 | 0 | Hydrophobic |
| C6 | CD2 | LEU- 89 | 4.2 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 92 | 4.16 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 92 | 4.4 | 0 | Hydrophobic |
| C19 | CD2 | LEU- 92 | 3.86 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 92 | 3.69 | 0 | Hydrophobic |
| C19 | CZ | PHE- 93 | 3.7 | 0 | Hydrophobic |
| C16 | CD1 | LEU- 98 | 4.17 | 0 | Hydrophobic |
| C18 | CD2 | LEU- 98 | 4 | 0 | Hydrophobic |
| C22 | CD1 | LEU- 98 | 3.71 | 0 | Hydrophobic |
| C18 | CE | MET- 99 | 3.96 | 0 | Hydrophobic |
| C3 | CD1 | ILE- 119 | 3.86 | 0 | Hydrophobic |
| C23 | CB | SER- 197 | 3.6 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 265 | 4.44 | 0 | Hydrophobic |
| C23 | CG | PRO- 266 | 4.42 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 305 | 4.47 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 305 | 3.9 | 0 | Hydrophobic |
| C11 | CG2 | VAL- 305 | 3.93 | 0 | Hydrophobic |
| C12 | CH2 | TRP- 310 | 4.15 | 0 | Hydrophobic |
| C21 | CH2 | TRP- 310 | 3.5 | 0 | Hydrophobic |
| O26 | O | HOH- 1636 | 3.41 | 143.2 | H-Bond (Protein Donor) |
