sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.750 Å
X-ray
2012-10-13
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.720 | 9.060 | 9.170 | 0.720 | 10.000 | 27 |
| Name: | Epidermal growth factor receptor |
|---|---|
| ID: | EGFR_HUMAN |
| AC: | P00533 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| A | 100 % |
| B-Factor: | 42.968 |
|---|---|
| Number of residues: | 32 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.170 | 496.125 |
| % Hydrophobic | % Polar |
|---|---|
| 57.14 | 42.86 |
| According to VolSite | |
| HET Code: | AQ4 |
|---|---|
| Formula: | C22H23N3O4 |
| Molecular weight: | 393.436 g/mol |
| DrugBank ID: | DB00530 |
| Buried Surface Area: | 59.75 % |
| Polar Surface area: | 74.73 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 1 |
| Rings: | 3 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 24.7702 | 9.19393 | -0.00331034 |
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 |
| C10 | CB | LEU- 694 | 4.17 | 0 | Hydrophobic |
| C14 | CD2 | LEU- 694 | 4.24 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 694 | 3.7 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 702 | 4.48 | 0 | Hydrophobic |
| C4 | CG1 | VAL- 702 | 3.7 | 0 | Hydrophobic |
| C2 | CB | ALA- 719 | 4.45 | 0 | Hydrophobic |
| C4 | CB | ALA- 719 | 4.04 | 0 | Hydrophobic |
| C3 | CB | LYS- 721 | 3.91 | 0 | Hydrophobic |
| C2 | CB | LYS- 721 | 3.48 | 0 | Hydrophobic |
| C22 | CD | LYS- 721 | 4.04 | 0 | Hydrophobic |
| C1 | CB | LEU- 764 | 3.95 | 0 | Hydrophobic |
| C1 | CG2 | THR- 766 | 3.64 | 0 | Hydrophobic |
| C17 | CD1 | LEU- 768 | 3.93 | 0 | Hydrophobic |
| C17 | CB | MET- 769 | 4.11 | 0 | Hydrophobic |
| N2 | N | MET- 769 | 2.92 | 161.25 | H-Bond (Protein Donor) |
| C11 | CB | CYS- 773 | 3.68 | 0 | Hydrophobic |
| C12 | CB | CYS- 773 | 3.81 | 0 | Hydrophobic |
| C12 | CB | ASP- 776 | 3.83 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 820 | 4.4 | 0 | Hydrophobic |
| C7 | CD2 | LEU- 820 | 3.82 | 0 | Hydrophobic |
| C20 | CG2 | THR- 830 | 3.67 | 0 | Hydrophobic |
