sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.900 Å
X-ray
2012-12-03
| 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: | 48.438 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 43 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.421 | 1208.250 |
| % Hydrophobic | % Polar |
|---|---|
| 53.07 | 46.93 |
| According to VolSite | |
| HET Code: | W2R |
|---|---|
| Formula: | C29H33ClN6O4 |
| Molecular weight: | 565.063 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 70.41 % |
| Polar Surface area: | 122.56 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 7 |
| H-Bond Donors: | 4 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 11 |
| X | Y | Z |
|---|---|---|
| 5.06665 | 1.1106 | 10.3492 |
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 |
| C12 | CD1 | LEU- 718 | 4.26 | 0 | Hydrophobic |
| C26 | CB | LEU- 718 | 4.43 | 0 | Hydrophobic |
| C20 | CD2 | PHE- 723 | 3.78 | 0 | Hydrophobic |
| C21 | CG | PHE- 723 | 4.21 | 0 | Hydrophobic |
| C22 | CE2 | PHE- 723 | 4.03 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 726 | 4.44 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 726 | 4.16 | 0 | Hydrophobic |
| C8 | CG1 | VAL- 726 | 3.85 | 0 | Hydrophobic |
| C8 | CB | ALA- 743 | 3.82 | 0 | Hydrophobic |
| C12 | CB | ALA- 743 | 4.24 | 0 | Hydrophobic |
| O36 | NZ | LYS- 745 | 2.82 | 168.1 | H-Bond (Protein Donor) |
| CL1 | CB | LYS- 745 | 3.67 | 0 | Hydrophobic |
| C17 | CB | LYS- 745 | 3.98 | 0 | Hydrophobic |
| C21 | CD2 | LEU- 747 | 3.9 | 0 | Hydrophobic |
| C7 | CE | MET- 766 | 4.3 | 0 | Hydrophobic |
| C2 | CE | MET- 766 | 3.64 | 0 | Hydrophobic |
| C15 | CD1 | LEU- 777 | 4.46 | 0 | Hydrophobic |
| CL1 | CB | LEU- 788 | 4.01 | 0 | Hydrophobic |
| C7 | CD1 | LEU- 788 | 3.73 | 0 | Hydrophobic |
| C4 | CB | THR- 790 | 4.38 | 0 | Hydrophobic |
| CL1 | CG2 | THR- 790 | 3.66 | 0 | Hydrophobic |
| C16 | CG2 | THR- 790 | 3.76 | 0 | Hydrophobic |
| C17 | CG2 | THR- 790 | 3.42 | 0 | Hydrophobic |
| N30 | N | MET- 793 | 2.97 | 166.55 | H-Bond (Protein Donor) |
| C29 | CB | CYS- 797 | 4.41 | 0 | Hydrophobic |
| C12 | CD2 | LEU- 844 | 4.01 | 0 | Hydrophobic |
| C27 | CD2 | LEU- 844 | 4.09 | 0 | Hydrophobic |
| C29 | CD2 | LEU- 844 | 3.79 | 0 | Hydrophobic |
| C3 | CG2 | THR- 854 | 3.88 | 0 | Hydrophobic |
| C5 | CB | THR- 854 | 4.28 | 0 | Hydrophobic |
| C28 | CG2 | THR- 854 | 3.55 | 0 | Hydrophobic |
| O37 | OD2 | ASP- 855 | 2.81 | 166.58 | H-Bond (Ligand Donor) |
| N34 | O | PHE- 856 | 2.91 | 147.98 | H-Bond (Ligand Donor) |
| N35 | O | GLY- 857 | 3.1 | 141.53 | H-Bond (Ligand Donor) |
| C23 | CB | LEU- 858 | 4.02 | 0 | Hydrophobic |
| C24 | CB | ALA- 859 | 4.37 | 0 | Hydrophobic |
| C20 | CB | LEU- 862 | 4 | 0 | Hydrophobic |
