sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.550 Å
X-ray
2015-07-17
| 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 | 3 % |
| B | 97 % |
| B-Factor: | 21.904 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 32 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | MG |
| Ligandability | Volume (Å3) |
|---|---|
| 0.395 | 2109.375 |
| % Hydrophobic | % Polar |
|---|---|
| 38.88 | 61.12 |
| According to VolSite | |
| HET Code: | ANP |
|---|---|
| Formula: | C10H13N6O12P3 |
| Molecular weight: | 502.164 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 67.78 % |
| Polar Surface area: | 322.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 16 |
| H-Bond Donors: | 4 |
| Rings: | 3 |
| Aromatic rings: | 2 |
| Anionic atoms: | 4 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| -31.3215 | -47.4855 | 16.1821 |
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 |
| C1' | CB | LEU- 694 | 4.28 | 0 | Hydrophobic |
| O3G | N | ALA- 698 | 2.89 | 165.68 | H-Bond (Protein Donor) |
| C5' | CG2 | VAL- 702 | 3.88 | 0 | Hydrophobic |
| O1A | NZ | LYS- 721 | 3.54 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 721 | 2.79 | 0 | Ionic (Protein Cationic) |
| O2A | NZ | LYS- 721 | 2.79 | 166.69 | H-Bond (Protein Donor) |
| N6 | O | GLN- 767 | 3.05 | 158.56 | H-Bond (Ligand Donor) |
| N1 | N | MET- 769 | 3.02 | 164.54 | H-Bond (Protein Donor) |
| C2' | CB | CYS- 773 | 4.07 | 0 | Hydrophobic |
| O2G | NE | ARG- 817 | 2.89 | 174.03 | H-Bond (Protein Donor) |
| O2G | CZ | ARG- 817 | 3.63 | 0 | Ionic (Protein Cationic) |
| O2G | ND2 | ASN- 818 | 3.34 | 137.18 | H-Bond (Protein Donor) |
| O1B | MG | MG- 1002 | 1.99 | 0 | Metal Acceptor |
| O2A | MG | MG- 1002 | 2.03 | 0 | Metal Acceptor |
| O2' | O | HOH- 1164 | 2.69 | 179.95 | H-Bond (Protein Donor) |
