sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.850 Å
X-ray
2014-10-03
| Min | Mean | Median | Standard Deviation | Max | Count | |
|---|---|---|---|---|---|---|
| pChEMBL: | 6.850 | 8.840 | 9.010 | 0.630 | 9.400 | 25 |
| 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: | 44.188 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 28 |
| Non Standard Amino Acids: | 1 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.311 | 479.250 |
| % Hydrophobic | % Polar |
|---|---|
| 56.34 | 43.66 |
| According to VolSite | |
| HET Code: | IRE |
|---|---|
| Formula: | C22H25ClFN4O3 |
| Molecular weight: | 447.910 g/mol |
| DrugBank ID: | DB00317 |
| Buried Surface Area: | 52.87 % |
| Polar Surface area: | 68.88 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 2 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 1.45748 | 194.208 | 20.4128 |
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 |
| CAA | CD2 | LEU- 718 | 3.52 | 0 | Hydrophobic |
| CAZ | CD1 | LEU- 718 | 3.75 | 0 | Hydrophobic |
| CAI | CG1 | VAL- 726 | 4.03 | 0 | Hydrophobic |
| CAG | CG1 | VAL- 726 | 4.31 | 0 | Hydrophobic |
| C5 | CB | ALA- 743 | 4.15 | 0 | Hydrophobic |
| CAG | CB | ALA- 743 | 4.21 | 0 | Hydrophobic |
| CL | CB | LYS- 745 | 3.41 | 0 | Hydrophobic |
| CAX | CB | LYS- 745 | 3.61 | 0 | Hydrophobic |
| CAW | CD | LYS- 745 | 3.58 | 0 | Hydrophobic |
| CAW | CD | LYS- 745 | 3.58 | 0 | Hydrophobic |
| CAW | CE | MET- 766 | 4.16 | 0 | Hydrophobic |
| FAB | SD | MET- 766 | 3.37 | 0 | Hydrophobic |
| CL | CB | LEU- 788 | 3.75 | 0 | Hydrophobic |
| FAB | CD1 | LEU- 788 | 3.63 | 0 | Hydrophobic |
| CL | CG2 | THR- 790 | 3.38 | 0 | Hydrophobic |
| CAX | CG2 | THR- 790 | 3.64 | 0 | Hydrophobic |
| CAH | CD1 | LEU- 792 | 3.91 | 0 | Hydrophobic |
| CAA | CD1 | LEU- 792 | 4.42 | 0 | Hydrophobic |
| CAH | CB | MET- 793 | 4.23 | 0 | Hydrophobic |
| N3 | N | MET- 793 | 2.98 | 161.76 | H-Bond (Protein Donor) |
| NBE | OD2 | ASP- 800 | 3.46 | 138.48 | H-Bond (Ligand Donor) |
| NBE | OD2 | ASP- 800 | 3.46 | 0 | Ionic (Ligand Cationic) |
| CAI | CD2 | LEU- 844 | 4.49 | 0 | Hydrophobic |
| C5 | CD1 | LEU- 844 | 3.73 | 0 | Hydrophobic |
| CAE | CG2 | THR- 854 | 4.21 | 0 | Hydrophobic |
