sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.300 Å
X-ray
2011-09-29
| 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 |
|---|---|
| A | 100 % |
| B-Factor: | 46.330 |
|---|---|
| Number of residues: | 17 |
| Including | |
| Standard Amino Acids: | 17 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.590 | 1103.625 |
| % Hydrophobic | % Polar |
|---|---|
| 55.96 | 44.04 |
| According to VolSite | |
| HET Code: | 4TT |
|---|---|
| Formula: | C14H13N3 |
| Molecular weight: | 223.273 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 50.79 % |
| Polar Surface area: | 44.47 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 1 |
| H-Bond Donors: | 2 |
| Rings: | 4 |
| Aromatic rings: | 3 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 0 |
| X | Y | Z |
|---|---|---|
| -2.00918 | 18.8548 | -29.7872 |
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 |
| C11 | CB | LEU- 840 | 3.93 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 840 | 4.03 | 0 | Hydrophobic |
| C11 | CG1 | VAL- 848 | 3.79 | 0 | Hydrophobic |
| N14 | O | GLU- 917 | 2.71 | 173.05 | H-Bond (Ligand Donor) |
| N4 | O | CYS- 919 | 2.66 | 120.22 | H-Bond (Ligand Donor) |
| N8 | N | CYS- 919 | 2.98 | 161.99 | H-Bond (Protein Donor) |
| C12 | CD2 | LEU- 1035 | 3.92 | 0 | Hydrophobic |
