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
2004-12-05
| 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: | 37.739 |
|---|---|
| Number of residues: | 29 |
| Including | |
| Standard Amino Acids: | 29 |
| Non Standard Amino Acids: | 0 |
| Water Molecules: | 0 |
| Cofactors: | |
| Metals: | |
| Ligandability | Volume (Å3) |
|---|---|
| 1.284 | 401.625 |
| % Hydrophobic | % Polar |
|---|---|
| 60.50 | 39.50 |
| According to VolSite | |
| HET Code: | AAZ |
|---|---|
| Formula: | C23H21N3O4S |
| Molecular weight: | 435.496 g/mol |
| DrugBank ID: | DB07334 |
| Buried Surface Area: | 51.7 % |
| Polar Surface area: | 102.7 Å2 |
| Number of | |
|---|---|
| H-Bond Acceptors: | 6 |
| H-Bond Donors: | 1 |
| Rings: | 4 |
| Aromatic rings: | 4 |
| Anionic atoms: | 0 |
| Cationic atoms: | 0 |
| Rule of Five Violation: | 0 |
| Rotatable Bonds: | 7 |
| X | Y | Z |
|---|---|---|
| 0.151387 | 30.335 | 18.3265 |
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 |
| C1 | CB | LEU- 838 | 4.26 | 0 | Hydrophobic |
| C11 | CD2 | LEU- 838 | 3.9 | 0 | Hydrophobic |
| C9 | CD2 | LEU- 838 | 3.61 | 0 | Hydrophobic |
| C22 | CG2 | VAL- 846 | 3.8 | 0 | Hydrophobic |
| C26 | CG2 | VAL- 846 | 3.33 | 0 | Hydrophobic |
| C23 | CG1 | VAL- 846 | 3.93 | 0 | Hydrophobic |
| C20 | CB | ALA- 864 | 4.11 | 0 | Hydrophobic |
| C20 | CG2 | VAL- 914 | 3.75 | 0 | Hydrophobic |
| C11 | CZ | PHE- 916 | 3.79 | 0 | Hydrophobic |
| N13 | O | CYS- 917 | 2.81 | 139.96 | H-Bond (Ligand Donor) |
| N15 | N | CYS- 917 | 3.07 | 153.49 | H-Bond (Protein Donor) |
| O4 | ND2 | ASN- 921 | 3.04 | 166.72 | H-Bond (Protein Donor) |
| C31 | CD2 | LEU- 1033 | 3.99 | 0 | Hydrophobic |
| C19 | CD1 | LEU- 1033 | 4.08 | 0 | Hydrophobic |
