sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.700 Å
X-ray
2007-11-01
| Name: | Vascular endothelial growth factor receptor 2 |
|---|---|
| ID: | VGFR2_HUMAN |
| AC: | P35968 |
| Organism: | Homo sapiens |
| Reign: | Eukaryota |
| TaxID: | 9606 |
| EC Number: | 2.7.10.1 |
| Chain Name: | Percentage of Residues within binding site |
|---|---|
| B | 100 % |
| B-Factor: | 25.121 |
|---|---|
| Number of residues: | 34 |
| Including | |
| Standard Amino Acids: | 34 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.154 | 563.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.69 | 44.31 |
| According to VolSite | |
| HET Code: | 887 |
|---|---|
| Formula: | C25H22N2O4 |
| Molecular weight: | 414.453 g/mol |
| DrugBank ID: | DB07274 |
| Buried Surface Area: | 69.74 % |
| Polar Surface area: | 69.68 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 1 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| -1.81852 | 38.661 | 67.683 |
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 |
| C34 | CD2 | LEU- 840 | 4.4 | 0 | Hydrophobic |
| C38 | CB | LEU- 840 | 3.98 | 0 | Hydrophobic |
| C27 | CD1 | LEU- 840 | 3.65 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 848 | 4.05 | 0 | Hydrophobic |
| C2 | CG1 | VAL- 848 | 3.93 | 0 | Hydrophobic |
| C26 | CG1 | VAL- 848 | 3.99 | 0 | Hydrophobic |
| C2 | CB | ALA- 866 | 4.4 | 0 | Hydrophobic |
| C23 | CB | ALA- 866 | 3.48 | 0 | Hydrophobic |
| C12 | CD | LYS- 868 | 4.47 | 0 | Hydrophobic |
| C10 | CB | LYS- 868 | 3.52 | 0 | Hydrophobic |
| DuAr | NZ | LYS- 868 | 3.98 | 16.48 | Pi/Cation |
| C12 | CG | GLU- 885 | 4.48 | 0 | Hydrophobic |
| C47 | CG | GLU- 885 | 3.32 | 0 | Hydrophobic |
| N43 | OE2 | GLU- 885 | 3.19 | 134.11 | H-Bond (Ligand Donor) |
| C47 | CG2 | ILE- 888 | 4.07 | 0 | Hydrophobic |
| C46 | CG | LEU- 889 | 3.61 | 0 | Hydrophobic |
| C12 | CD1 | LEU- 889 | 3.63 | 0 | Hydrophobic |
| C5 | CG2 | VAL- 899 | 4.44 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 914 | 3.6 | 0 | Hydrophobic |
| C11 | CG2 | THR- 916 | 3.66 | 0 | Hydrophobic |
| C34 | CZ | PHE- 918 | 3.91 | 0 | Hydrophobic |
| N21 | N | CYS- 919 | 2.85 | 145.07 | H-Bond (Protein Donor) |
| C29 | CB | CYS- 919 | 4.3 | 0 | Hydrophobic |
| C6 | CD1 | LEU- 1035 | 4.37 | 0 | Hydrophobic |
| C29 | CD1 | LEU- 1035 | 4.48 | 0 | Hydrophobic |
| C23 | CD1 | LEU- 1035 | 3.49 | 0 | Hydrophobic |
| C18 | CD1 | LEU- 1035 | 3.56 | 0 | Hydrophobic |
| C5 | CB | CYS- 1045 | 3.69 | 0 | Hydrophobic |
| C6 | SG | CYS- 1045 | 3.93 | 0 | Hydrophobic |
| O45 | N | ASP- 1046 | 2.71 | 165.21 | H-Bond (Protein Donor) |
| C46 | CE1 | PHE- 1047 | 3.57 | 0 | Hydrophobic |
| C47 | CD2 | LEU- 1049 | 3.75 | 0 | Hydrophobic |
