sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.750 Å
X-ray
2007-11-16
| 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: | 17.768 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 37 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.457 | 445.500 |
| % Hydrophobic | % Polar |
|---|---|
| 68.18 | 31.82 |
| According to VolSite | |
| HET Code: | RAJ |
|---|---|
| Formula: | C29H30F3N6O |
| Molecular weight: | 535.583 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 61.31 % |
| Polar Surface area: | 84.24 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 10 |
| X | Y | Z |
|---|---|---|
| 36.0873 | 33.3927 | 11.2011 |
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 |
| C6 | CB | LEU- 840 | 4.08 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 840 | 3.78 | 0 | Hydrophobic |
| C16 | CG1 | VAL- 848 | 3.95 | 0 | Hydrophobic |
| C5 | CG1 | VAL- 848 | 3.96 | 0 | Hydrophobic |
| C16 | CB | ALA- 866 | 3.81 | 0 | Hydrophobic |
| C5 | CB | ALA- 866 | 4.41 | 0 | Hydrophobic |
| C2 | CB | ALA- 866 | 4.5 | 0 | Hydrophobic |
| C16 | CB | LYS- 868 | 3.91 | 0 | Hydrophobic |
| C19 | CG | GLU- 885 | 3.7 | 0 | Hydrophobic |
| C26 | CG | GLU- 885 | 3.99 | 0 | Hydrophobic |
| N5 | OE2 | GLU- 885 | 2.88 | 136.74 | H-Bond (Ligand Donor) |
| C25 | CG2 | ILE- 888 | 4.44 | 0 | Hydrophobic |
| C13 | CD1 | LEU- 889 | 4.29 | 0 | Hydrophobic |
| C23 | CD2 | LEU- 889 | 3.9 | 0 | Hydrophobic |
| F3 | CD1 | ILE- 892 | 4.03 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 898 | 3.69 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 899 | 4.31 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 899 | 4.34 | 0 | Hydrophobic |
| C12 | CG1 | VAL- 899 | 4.34 | 0 | Hydrophobic |
| C14 | CG1 | VAL- 914 | 4.3 | 0 | Hydrophobic |
| C15 | CG2 | THR- 916 | 3.52 | 0 | Hydrophobic |
| N2 | N | CYS- 919 | 2.86 | 171.68 | H-Bond (Protein Donor) |
| F2 | CD1 | LEU- 1019 | 4.33 | 0 | Hydrophobic |
| F3 | CD1 | LEU- 1019 | 3.8 | 0 | Hydrophobic |
| C2 | CD1 | LEU- 1035 | 3.98 | 0 | Hydrophobic |
| F2 | CG2 | ILE- 1044 | 3.88 | 0 | Hydrophobic |
| F1 | CG2 | ILE- 1044 | 4.08 | 0 | Hydrophobic |
| N6 | OD1 | ASP- 1046 | 3.99 | 0 | Ionic (Ligand Cationic) |
| O1 | N | ASP- 1046 | 2.95 | 168.45 | H-Bond (Protein Donor) |
| F2 | CB | ASP- 1046 | 3.76 | 0 | Hydrophobic |
| C22 | CB | ASP- 1046 | 3.8 | 0 | Hydrophobic |
