sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
1.640 Å
X-ray
2012-01-17
| 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: | 23.145 |
|---|---|
| Number of residues: | 44 |
| Including | |
| Standard Amino Acids: | 44 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.399 | 891.000 |
| % Hydrophobic | % Polar |
|---|---|
| 54.92 | 45.08 |
| According to VolSite | |
| HET Code: | 0JA |
|---|---|
| Formula: | C27H19ClFN5O3S |
| Molecular weight: | 547.988 g/mol |
| DrugBank ID: | - |
| Buried Surface Area: | 66.94 % |
| Polar Surface area: | 145.23 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 2 |
| Rings: | 6 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 2 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 26.7592 | -28.6096 | -14.3383 |
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 |
| C18 | CD2 | LEU- 840 | 4.22 | 0 | Hydrophobic |
| S19 | CD1 | LEU- 840 | 3.84 | 0 | Hydrophobic |
| C4 | CG2 | VAL- 848 | 3.75 | 0 | Hydrophobic |
| C4 | CB | ALA- 866 | 4.31 | 0 | Hydrophobic |
| C9 | CB | ALA- 866 | 3.42 | 0 | Hydrophobic |
| C3 | CB | LYS- 868 | 3.45 | 0 | Hydrophobic |
| N24 | OE2 | GLU- 885 | 2.92 | 137.75 | H-Bond (Ligand Donor) |
| C28 | CG | GLU- 885 | 3.89 | 0 | Hydrophobic |
| F1 | CD1 | LEU- 889 | 3.55 | 0 | Hydrophobic |
| CL3 | CD2 | LEU- 889 | 4.04 | 0 | Hydrophobic |
| C31 | CD2 | LEU- 889 | 3.69 | 0 | Hydrophobic |
| C32 | CD2 | LEU- 889 | 3.6 | 0 | Hydrophobic |
| C35 | CD1 | ILE- 892 | 4.25 | 0 | Hydrophobic |
| CL3 | CG1 | VAL- 898 | 3.82 | 0 | Hydrophobic |
| C36 | CG1 | VAL- 898 | 4.42 | 0 | Hydrophobic |
| CL3 | CG2 | VAL- 899 | 3.32 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 914 | 3.3 | 0 | Hydrophobic |
| F1 | CG1 | VAL- 916 | 3.32 | 0 | Hydrophobic |
| C8 | CG2 | VAL- 916 | 3.55 | 0 | Hydrophobic |
| C3 | CG2 | VAL- 916 | 3.39 | 0 | Hydrophobic |
| C16 | CZ | PHE- 918 | 3.78 | 0 | Hydrophobic |
| N11 | N | CYS- 919 | 3.16 | 166.26 | H-Bond (Protein Donor) |
| N13 | O | CYS- 919 | 2.75 | 155.39 | H-Bond (Ligand Donor) |
| C35 | CD2 | LEU- 1019 | 4.13 | 0 | Hydrophobic |
| C36 | CD1 | LEU- 1019 | 3.83 | 0 | Hydrophobic |
| C9 | CD1 | LEU- 1035 | 3.44 | 0 | Hydrophobic |
| C36 | CG2 | ILE- 1044 | 4.23 | 0 | Hydrophobic |
| O26 | N | ASP- 1046 | 2.8 | 167.81 | H-Bond (Protein Donor) |
| C28 | CB | ASP- 1046 | 3.54 | 0 | Hydrophobic |
| S19 | CE1 | PHE- 1047 | 4.32 | 0 | Hydrophobic |
