sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.530 Å
X-ray
2013-06-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 4.660 | 4.660 | 4.660 | 0.000 | 4.660 | 2 |
| Name: | Egl nine homolog 1 |
|---|---|
| ID: | EGLN1_HUMAN |
| AC: | Q9GZT9 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | / |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 17.283 |
|---|---|
| Number of residues: | 31 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | FE2 |
| Ligandability | Volume (Å3) |
|---|---|
| 0.300 | 297.000 |
| % Hydrophobic | % Polar |
|---|---|
| 59.09 | 40.91 |
| According to VolSite | |
| HET Code: | FNT |
|---|---|
| Formula: | C13H10ClN2O4 |
| Molecular weight: | 293.683 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 65.31 % |
| Polar Surface area: | 102.35 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 2 |
| Rings: | 2 |
| Aromatic rings: | 2 |
| Anionic atoms: | 1 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 3 |
| X | Y | Z |
|---|---|---|
| -40.2207 | -19.3738 | 3.87895 |
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 | CG2 | ILE- 256 | 3.72 | 0 | Hydrophobic |
| C6 | SD | MET- 299 | 3.68 | 0 | Hydrophobic |
| C4 | CE | MET- 299 | 3.42 | 0 | Hydrophobic |
| O19 | OH | TYR- 303 | 2.63 | 161.64 | H-Bond (Protein Donor) |
| CL1 | CZ | TYR- 310 | 4.36 | 0 | Hydrophobic |
| C08 | CD1 | ILE- 327 | 3.54 | 0 | Hydrophobic |
| O18 | OH | TYR- 329 | 2.64 | 173.05 | H-Bond (Protein Donor) |
| C08 | CD1 | LEU- 343 | 3.81 | 0 | Hydrophobic |
| C08 | CE2 | PHE- 366 | 4.42 | 0 | Hydrophobic |
| O17 | CZ | ARG- 383 | 3.67 | 0 | Ionic (Protein Cationic) |
| O18 | CZ | ARG- 383 | 3.59 | 0 | Ionic (Protein Cationic) |
| O17 | NH1 | ARG- 383 | 2.8 | 161.74 | H-Bond (Protein Donor) |
| O18 | NH2 | ARG- 383 | 2.82 | 173.34 | H-Bond (Protein Donor) |
| O18 | NH1 | ARG- 383 | 3.48 | 131.63 | H-Bond (Protein Donor) |
| CL1 | CZ2 | TRP- 389 | 4.18 | 0 | Hydrophobic |
| N8 | FE | FE2- 501 | 2.31 | 0 | Metal Acceptor |
| O13 | FE | FE2- 501 | 2.26 | 0 | Metal Acceptor |
| DuAr | FE | FE2- 501 | 3.65 | 89.57 | Pi/Cation |
