sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.100 Å
X-ray
2007-08-03
| 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: | 32.936 |
|---|---|
| Number of residues: | 37 |
| Including | |
| Standard Amino Acids: | 36 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 1 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.664 | 823.500 |
| % Hydrophobic | % Polar |
|---|---|
| 60.25 | 39.75 |
| According to VolSite | |
| HET Code: | 857 |
|---|---|
| Formula: | C26H27ClN5O4 |
| Molecular weight: | 508.977 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 63.42 % |
| Polar Surface area: | 102.95 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 3 |
| Rings: | 5 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 1 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 8 |
| X | Y | Z |
|---|---|---|
| 38.6178 | 35.1128 | 12.7126 |
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 |
| N1 | O | HOH- 200 | 2.76 | 156.7 | H-Bond (Ligand Donor) |
| C12 | CD1 | LEU- 840 | 4.01 | 0 | Hydrophobic |
| C13 | CG1 | VAL- 848 | 4.27 | 0 | Hydrophobic |
| C1 | CG1 | VAL- 848 | 3.37 | 0 | Hydrophobic |
| C8 | CB | ALA- 866 | 3.44 | 0 | Hydrophobic |
| C1 | CB | ALA- 866 | 3.87 | 0 | Hydrophobic |
| C17 | CB | LYS- 868 | 3.84 | 0 | Hydrophobic |
| C6 | CG | GLU- 885 | 4.16 | 0 | Hydrophobic |
| C23 | CG | GLU- 885 | 4.23 | 0 | Hydrophobic |
| N2 | OE2 | GLU- 885 | 2.93 | 149.8 | H-Bond (Ligand Donor) |
| C4 | CG2 | ILE- 888 | 3.98 | 0 | Hydrophobic |
| C25 | CD2 | LEU- 889 | 3.95 | 0 | Hydrophobic |
| C21 | CG1 | VAL- 898 | 4.14 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 899 | 4.14 | 0 | Hydrophobic |
| C24 | CG1 | VAL- 899 | 3.57 | 0 | Hydrophobic |
| C17 | CG2 | THR- 916 | 3.54 | 0 | Hydrophobic |
| N3 | N | CYS- 919 | 3.19 | 169.46 | H-Bond (Protein Donor) |
| N5 | O | CYS- 919 | 2.62 | 124.73 | H-Bond (Ligand Donor) |
| CL | CD1 | LEU- 1019 | 3.55 | 0 | Hydrophobic |
| C3 | CB | CYS- 1024 | 4.37 | 0 | Hydrophobic |
| C8 | CD1 | LEU- 1035 | 3.48 | 0 | Hydrophobic |
| C24 | CB | CYS- 1045 | 4.31 | 0 | Hydrophobic |
| C14 | CB | CYS- 1045 | 3.76 | 0 | Hydrophobic |
| N4 | N | ASP- 1046 | 3.05 | 162.81 | H-Bond (Protein Donor) |
| C23 | CB | ASP- 1046 | 4.5 | 0 | Hydrophobic |
| C6 | CB | ASP- 1046 | 3.77 | 0 | Hydrophobic |
