sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
2.950 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: | 53.738 |
|---|---|
| Number of residues: | 38 |
| Including | |
| Standard Amino Acids: | 38 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.107 | 276.750 |
| % Hydrophobic | % Polar |
|---|---|
| 67.07 | 32.93 |
| According to VolSite | |
| HET Code: | 276 |
|---|---|
| Formula: | C21H15ClF3N5O2 |
| Molecular weight: | 461.824 g/mol |
| DrugBank ID: | DB06938 |
| Buried Surface Area: | 73.23 % |
| Polar Surface area: | 91.93 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 5 |
| H-Bond Donors: | 3 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 1 |
| Rotatable Bonds: | 6 |
| X | Y | Z |
|---|---|---|
| 65.6729 | 94.1472 | 44.8252 |
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 |
| C5 | CD1 | LEU- 840 | 3.89 | 0 | Hydrophobic |
| C6 | CG1 | VAL- 848 | 4.3 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 848 | 3.72 | 0 | Hydrophobic |
| C1 | CB | ALA- 866 | 3.34 | 0 | Hydrophobic |
| C23 | CB | ALA- 866 | 4 | 0 | Hydrophobic |
| C22 | CB | LYS- 868 | 3.74 | 0 | Hydrophobic |
| N29 | OE2 | GLU- 885 | 2.86 | 120.67 | H-Bond (Ligand Donor) |
| N32 | OE2 | GLU- 885 | 3.1 | 134.04 | H-Bond (Ligand Donor) |
| F47 | CG | GLU- 885 | 4.43 | 0 | Hydrophobic |
| C34 | CG | GLU- 885 | 3.96 | 0 | Hydrophobic |
| F45 | CG2 | ILE- 888 | 3.57 | 0 | Hydrophobic |
| F45 | CD2 | LEU- 889 | 4.07 | 0 | Hydrophobic |
| C36 | CD2 | LEU- 889 | 3.77 | 0 | Hydrophobic |
| CL44 | CD1 | ILE- 892 | 4.28 | 0 | Hydrophobic |
| F45 | CD1 | ILE- 892 | 3.34 | 0 | Hydrophobic |
| CL44 | CG1 | VAL- 898 | 3.79 | 0 | Hydrophobic |
| C1 | CG2 | VAL- 899 | 4.21 | 0 | Hydrophobic |
| C38 | CG1 | VAL- 899 | 3.55 | 0 | Hydrophobic |
| C22 | CG2 | THR- 916 | 3.45 | 0 | Hydrophobic |
| N3 | N | CYS- 919 | 3.03 | 156.88 | H-Bond (Protein Donor) |
| N12 | O | CYS- 919 | 2.74 | 120.03 | H-Bond (Ligand Donor) |
| CL44 | CD2 | LEU- 1019 | 3.59 | 0 | Hydrophobic |
| F46 | CD2 | LEU- 1019 | 4.37 | 0 | Hydrophobic |
| F46 | CB | HIS- 1026 | 4.34 | 0 | Hydrophobic |
| C1 | CD1 | LEU- 1035 | 3.65 | 0 | Hydrophobic |
| CL44 | CG2 | ILE- 1044 | 3.96 | 0 | Hydrophobic |
| C19 | CB | CYS- 1045 | 4.08 | 0 | Hydrophobic |
| C38 | CB | CYS- 1045 | 4.25 | 0 | Hydrophobic |
| N27 | N | ASP- 1046 | 3.06 | 159.42 | H-Bond (Protein Donor) |
| C33 | CB | ASP- 1046 | 4.02 | 0 | Hydrophobic |
